HEADER PROTEIN FIBRIL 06-NOV-13 4NIN
TITLE DSVISLS SEGMENT 101-107 FROM HUMAN SUPEROXIDE DISMUTASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DSVISLS SEGMENT FROM SUPEROXIDE DISMUTASE [CU-ZN];
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 102-108;
COMPND 5 SYNONYM: SUPEROXIDE DISMUTASE 1, HSOD1;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606
KEYWDS STERIC ZIPPER, CROSS-BETA SPINE, AMYLOID FIBER, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR S.A.SIEVERS,M.R.SAWAYA,D.EISENBERG
REVDAT 4 28-FEB-24 4NIN 1 REMARK LINK
REVDAT 3 22-NOV-17 4NIN 1 REMARK
REVDAT 2 22-JAN-14 4NIN 1 JRNL
REVDAT 1 04-DEC-13 4NIN 0
JRNL AUTH M.I.IVANOVA,S.A.SIEVERS,E.L.GUENTHER,L.M.JOHNSON,
JRNL AUTH 2 D.D.WINKLER,A.GALALELDEEN,M.R.SAWAYA,P.J.HART,D.S.EISENBERG
JRNL TITL AGGREGATION-TRIGGERING SEGMENTS OF SOD1 FIBRIL FORMATION
JRNL TITL 2 SUPPORT A COMMON PATHWAY FOR FAMILIAL AND SPORADIC ALS.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 197 2014
JRNL REFN ISSN 0027-8424
JRNL PMID 24344300
JRNL DOI 10.1073/PNAS.1320786110
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.7.1_743
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.67
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.660
REMARK 3 COMPLETENESS FOR RANGE (%) : 74.1
REMARK 3 NUMBER OF REFLECTIONS : 705
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.191
REMARK 3 R VALUE (WORKING SET) : 0.187
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.220
REMARK 3 FREE R VALUE TEST SET COUNT : 65
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 22.6715 - 1.4023 0.74 640 65 0.1872 0.2281
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.10
REMARK 3 SHRINKAGE RADIUS : 0.83
REMARK 3 K_SOL : 0.44
REMARK 3 B_SOL : 58.79
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.160
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 11.41
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.28
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -4.91060
REMARK 3 B22 (A**2) : -5.65070
REMARK 3 B33 (A**2) : 10.56130
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -2.58500
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 49
REMARK 3 ANGLE : 0.923 66
REMARK 3 CHIRALITY : 0.061 10
REMARK 3 PLANARITY : 0.002 8
REMARK 3 DIHEDRAL : 10.205 17
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4NIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-13.
REMARK 100 THE DEPOSITION ID IS D_1000083250.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-JUL-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-E
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE
REMARK 200 CRYSTAL SI(220)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 717
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 73.6
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.18600
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 24.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51
REMARK 200 COMPLETENESS FOR SHELL (%) : 28.4
REMARK 200 DATA REDUNDANCY IN SHELL : 1.50
REMARK 200 R MERGE FOR SHELL (I) : 0.16600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.1.4
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 26.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 20% PEG 6000, AND 5
REMARK 280 MM ZNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.66850
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300 REMARK: BIOLOGICAL UNIT IS A PAIR OF BETA-SHEETS FORMED BY THE
REMARK 300 SYMMETRY OPERATORS X,Y,Z AND X,Y,Z-1 WITH POSITIVE AND NEGATIVE
REMARK 300 UNIT CELL TRANSLATIONS ALONG THE X AXIS. FOR EXAMPLE ONE SHEET IS
REMARK 300 COMPOSED OF SYMMETRY OPERATORS X,Y,Z; X+1,Y,Z; X-1,Y,Z; X+2,Y,Z; X-
REMARK 300 2,Y,Z: THE OPPOSING SHEET IS COMPOSED OF SYMMETRY OPERATORS X,Y,Z-1;
REMARK 300 X+1,Y,Z-1; X-1,Y,Z-1; X+2,Y,Z-1; X-2,Y,Z-1, ETC.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 4.80500
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.61000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -9.61000
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 -4.80500
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 2.06314
REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -11.11006
REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 6.86814
REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -11.11006
REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 11.67314
REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -11.11006
REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 -7.54686
REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -11.11006
REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 -2.74186
REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -11.11006
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 1 OD1
REMARK 620 2 ASP A 1 N 89.0
REMARK 620 3 HOH A 201 O 85.9 163.4
REMARK 620 4 HOH A 202 O 80.3 76.7 86.9
REMARK 620 5 HOH A 203 O 103.2 102.6 93.9 176.5
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4NIO RELATED DB: PDB
REMARK 900 RELATED ID: 4NIP RELATED DB: PDB
DBREF 4NIN A 1 7 UNP P00441 SODC_HUMAN 102 108
SEQRES 1 A 7 ASP SER VAL ILE SER LEU SER
HET ZN A 101 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
FORMUL 3 HOH *4(H2 O)
LINK OD1 ASP A 1 ZN ZN A 101 1555 1555 2.05
LINK N ASP A 1 ZN ZN A 101 1555 1555 2.25
LINK ZN ZN A 101 O HOH A 201 1555 1555 2.17
LINK ZN ZN A 101 O HOH A 202 1555 1555 2.06
LINK ZN ZN A 101 O HOH A 203 1555 1555 2.22
SITE 1 AC1 4 ASP A 1 HOH A 201 HOH A 202 HOH A 203
CRYST1 4.805 45.337 11.300 90.00 100.52 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.208117 0.000000 0.038632 0.00000
SCALE2 0.000000 0.022057 0.000000 0.00000
SCALE3 0.000000 0.000000 0.090007 0.00000
ATOM 1 N ASP A 1 -0.909 -2.105 10.037 1.00 22.52 N
ATOM 2 CA ASP A 1 -0.241 -3.339 9.628 1.00 21.40 C
ATOM 3 C ASP A 1 -0.954 -3.918 8.405 1.00 21.39 C
ATOM 4 O ASP A 1 -2.162 -3.730 8.249 1.00 20.97 O
ATOM 5 CB ASP A 1 -0.241 -4.360 10.776 1.00 20.70 C
ATOM 6 CG ASP A 1 0.853 -4.097 11.803 1.00 23.34 C
ATOM 7 OD1 ASP A 1 1.312 -2.937 11.897 1.00 23.45 O
ATOM 8 OD2 ASP A 1 1.266 -5.052 12.509 1.00 21.37 O
ATOM 9 N SER A 2 -0.212 -4.615 7.541 1.00 19.32 N
ATOM 10 CA SER A 2 -0.807 -5.258 6.365 1.00 17.01 C
ATOM 11 C SER A 2 -0.117 -6.570 6.036 1.00 18.23 C
ATOM 12 O SER A 2 1.103 -6.695 6.181 1.00 16.86 O
ATOM 13 CB SER A 2 -0.770 -4.340 5.140 1.00 20.81 C
ATOM 14 OG SER A 2 0.489 -4.389 4.488 1.00 22.96 O
ATOM 15 N VAL A 3 -0.903 -7.547 5.589 1.00 15.43 N
ATOM 16 CA VAL A 3 -0.351 -8.816 5.147 1.00 15.59 C
ATOM 17 C VAL A 3 -0.951 -9.208 3.795 1.00 16.60 C
ATOM 18 O VAL A 3 -2.161 -9.083 3.598 1.00 14.52 O
ATOM 19 CB VAL A 3 -0.666 -9.944 6.156 1.00 15.87 C
ATOM 20 CG1 VAL A 3 -0.320 -11.295 5.561 1.00 18.07 C
ATOM 21 CG2 VAL A 3 0.062 -9.718 7.473 1.00 15.23 C
ATOM 22 N ILE A 4 -0.103 -9.667 2.870 1.00 13.73 N
ATOM 23 CA ILE A 4 -0.569 -10.362 1.671 1.00 13.89 C
ATOM 24 C ILE A 4 -0.016 -11.774 1.693 1.00 16.10 C
ATOM 25 O ILE A 4 1.197 -11.969 1.768 1.00 14.23 O
ATOM 26 CB ILE A 4 -0.119 -9.684 0.366 1.00 14.39 C
ATOM 27 CG1 ILE A 4 -0.751 -8.298 0.241 1.00 15.53 C
ATOM 28 CG2 ILE A 4 -0.508 -10.547 -0.839 1.00 15.49 C
ATOM 29 CD1 ILE A 4 -0.252 -7.514 -0.960 1.00 17.74 C
ATOM 30 N SER A 5 -0.907 -12.759 1.635 1.00 15.29 N
ATOM 31 CA SER A 5 -0.490 -14.149 1.693 1.00 17.76 C
ATOM 32 C SER A 5 -1.093 -14.951 0.561 1.00 17.82 C
ATOM 33 O SER A 5 -2.318 -15.051 0.455 1.00 16.66 O
ATOM 34 CB SER A 5 -0.909 -14.789 3.022 1.00 19.08 C
ATOM 35 OG SER A 5 -0.556 -16.164 3.035 1.00 21.03 O
ATOM 36 N LEU A 6 -0.228 -15.527 -0.270 1.00 16.86 N
ATOM 37 CA LEU A 6 -0.650 -16.487 -1.280 1.00 19.28 C
ATOM 38 C LEU A 6 -0.110 -17.859 -0.896 1.00 19.33 C
ATOM 39 O LEU A 6 1.091 -18.025 -0.702 1.00 18.71 O
ATOM 40 CB LEU A 6 -0.146 -16.087 -2.667 1.00 16.52 C
ATOM 41 CG LEU A 6 -0.839 -14.931 -3.390 1.00 23.35 C
ATOM 42 CD1 LEU A 6 -0.640 -13.614 -2.656 1.00 20.86 C
ATOM 43 CD2 LEU A 6 -0.327 -14.826 -4.832 1.00 24.01 C
ATOM 44 N SER A 7 -0.996 -18.841 -0.769 1.00 19.41 N
ATOM 45 CA SER A 7 -0.557 -20.177 -0.347 1.00 22.53 C
ATOM 46 C SER A 7 -1.191 -21.324 -1.147 1.00 23.93 C
ATOM 47 O SER A 7 -0.718 -22.473 -1.105 1.00 22.44 O
ATOM 48 CB SER A 7 -0.783 -20.377 1.163 1.00 23.32 C
ATOM 49 OG SER A 7 -2.145 -20.169 1.515 1.00 28.39 O
ATOM 50 OXT SER A 7 -2.182 -21.133 -1.861 1.00 24.28 O
TER 51 SER A 7
HETATM 52 ZN ZN A 101 -0.098 -1.456 12.027 0.55 15.51 ZN2+
HETATM 53 O HOH A 201 1.149 -0.620 13.588 1.00 22.73 O
HETATM 54 O HOH A 202 1.199 -0.584 10.679 1.00 22.47 O
HETATM 55 O HOH A 203 -1.582 -2.294 13.450 1.00 23.77 O
HETATM 56 O HOH A 204 1.870 -17.527 2.405 1.00 22.18 O
CONECT 1 52
CONECT 7 52
CONECT 52 1 7 53 54
CONECT 52 55
CONECT 53 52
CONECT 54 52
CONECT 55 52
MASTER 236 0 1 0 0 0 1 6 55 1 7 1
END