HEADER PROTEIN FIBRIL 15-JUN-11 3SGS
TITLE AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN RESIDUES 95-100
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-CRYSTALLIN B CHAIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ALPHA(B)-CRYSTALLIN, HEAT SHOCK PROTEIN BETA-5, HSPB5, RENAL
COMPND 5 CARCINOMA ANTIGEN NY-REN-27, ROSENTHAL FIBER COMPONENT;
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;
SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE
KEYWDS AMYLOID, AMYLOID FIBRIL, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR A.LAGANOWSKY,M.R.SAWAYA,D.CASCIO,D.EISENBERG
REVDAT 2 28-FEB-24 3SGS 1 REMARK
REVDAT 1 21-MAR-12 3SGS 0
JRNL AUTH A.LAGANOWSKY,C.LIU,M.R.SAWAYA,J.P.WHITELEGGE,J.PARK,M.ZHAO,
JRNL AUTH 2 A.PENSALFINI,A.B.SORIAGA,M.LANDAU,P.K.TENG,D.CASCIO,C.GLABE,
JRNL AUTH 3 D.EISENBERG
JRNL TITL ATOMIC VIEW OF A TOXIC AMYLOID SMALL OLIGOMER.
JRNL REF SCIENCE V. 335 1228 2012
JRNL REFN ISSN 0036-8075
JRNL PMID 22403391
JRNL DOI 10.1126/SCIENCE.1213151
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.27
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 3 NUMBER OF REFLECTIONS : 428
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.213
REMARK 3 R VALUE (WORKING SET) : 0.212
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 43
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 5
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90
REMARK 3 REFLECTION IN BIN (WORKING SET) : 99
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2920
REMARK 3 BIN FREE R VALUE SET COUNT : 11
REMARK 3 BIN FREE R VALUE : 0.2010
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 44
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 2
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.92
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.02000
REMARK 3 B22 (A**2) : 0.03000
REMARK 3 B33 (A**2) : -0.01000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.01000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.181
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.719
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 43 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 23 ; 0.007 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 58 ; 1.130 ; 2.047
REMARK 3 BOND ANGLES OTHERS (DEGREES): 59 ; 0.709 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 6.282 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 2 ;28.623 ;30.000
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 7 ;15.268 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 8 ; 0.049 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 47 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 5 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 29 ; 0.994 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 12 ; 0.085 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 47 ; 1.697 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 14 ; 0.751 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 11 ; 1.195 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3SGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-11.
REMARK 100 THE DEPOSITION ID IS D_1000066182.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-FEB-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
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) : 0.97918
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
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 : 438
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 90.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : 0.17800
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 24.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 5.00
REMARK 200 R MERGE FOR SHELL (I) : 0.38600
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
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1M DL-MALIC ACID PH 7.0, VAPOR
REMARK 280 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 9.75000
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 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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3SGM RELATED DB: PDB
REMARK 900 BROMODERIVATIVE-2 OF AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN
REMARK 900 RESIDUES 90-100
REMARK 900 RELATED ID: 3SGN RELATED DB: PDB
REMARK 900 BROMODERIVATIVE-8 OF AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN
REMARK 900 RESIDUES 90-100
REMARK 900 RELATED ID: 3SGO RELATED DB: PDB
REMARK 900 AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN RESIDUES 90-100
REMARK 900 RELATED ID: 3SGP RELATED DB: PDB
REMARK 900 AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN RESIDUES 90-100 MUTANT
REMARK 900 V91L
REMARK 900 RELATED ID: 3SGR RELATED DB: PDB
REMARK 900 TANDEM REPEAT OF AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN
REMARK 900 RESIDUES 90-100 MUTANT V91L
DBREF 3SGS A 1 6 UNP P02511 CRYAB_HUMAN 95 100
SEQRES 1 A 6 GLY ASP VAL ILE GLU VAL
FORMUL 2 HOH *2(H2 O)
CRYST1 4.821 19.500 21.004 90.00 94.23 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 0.207426 0.000000 0.015331 0.00000
SCALE2 0.000000 0.051282 0.000000 0.00000
SCALE3 0.000000 0.000000 0.047740 0.00000
ATOM 1 N GLY A 1 2.186 -1.809 10.234 1.00 10.29 N
ATOM 2 CA GLY A 1 2.320 -0.815 9.141 1.00 9.80 C
ATOM 3 C GLY A 1 1.418 -1.163 7.979 1.00 9.53 C
ATOM 4 O GLY A 1 0.509 -1.993 8.106 1.00 10.48 O
ATOM 5 N ASP A 2 1.661 -0.515 6.852 1.00 8.39 N
ATOM 6 CA ASP A 2 0.811 -0.643 5.673 1.00 7.85 C
ATOM 7 C ASP A 2 1.470 -1.495 4.602 1.00 6.99 C
ATOM 8 O ASP A 2 2.696 -1.595 4.534 1.00 6.68 O
ATOM 9 CB ASP A 2 0.516 0.739 5.087 1.00 7.92 C
ATOM 10 CG ASP A 2 -0.103 1.696 6.094 1.00 8.88 C
ATOM 11 OD1 ASP A 2 -0.972 1.260 6.879 1.00 9.26 O
ATOM 12 OD2 ASP A 2 0.269 2.895 6.083 1.00 9.54 O
ATOM 13 N VAL A 3 0.639 -2.089 3.747 1.00 5.97 N
ATOM 14 CA VAL A 3 1.107 -2.730 2.539 1.00 5.50 C
ATOM 15 C VAL A 3 0.524 -1.988 1.346 1.00 5.36 C
ATOM 16 O VAL A 3 -0.705 -1.905 1.195 1.00 4.65 O
ATOM 17 CB VAL A 3 0.686 -4.205 2.485 1.00 5.06 C
ATOM 18 CG1 VAL A 3 1.198 -4.839 1.211 1.00 5.22 C
ATOM 19 CG2 VAL A 3 1.197 -4.950 3.727 1.00 5.82 C
ATOM 20 N ILE A 4 1.395 -1.423 0.522 1.00 5.14 N
ATOM 21 CA ILE A 4 0.955 -0.615 -0.606 1.00 5.38 C
ATOM 22 C ILE A 4 1.465 -1.216 -1.907 1.00 5.88 C
ATOM 23 O ILE A 4 2.673 -1.309 -2.125 1.00 5.24 O
ATOM 24 CB ILE A 4 1.414 0.853 -0.480 1.00 4.86 C
ATOM 25 CG1 ILE A 4 0.807 1.508 0.765 1.00 6.05 C
ATOM 26 CG2 ILE A 4 0.992 1.652 -1.697 1.00 3.89 C
ATOM 27 CD1 ILE A 4 1.343 2.897 1.039 1.00 7.01 C
ATOM 28 N GLU A 5 0.522 -1.599 -2.768 1.00 7.64 N
ATOM 29 CA GLU A 5 0.797 -2.207 -4.071 1.00 9.57 C
ATOM 30 C GLU A 5 0.245 -1.323 -5.182 1.00 11.31 C
ATOM 31 O GLU A 5 -0.967 -1.167 -5.324 1.00 11.92 O
ATOM 32 CB GLU A 5 0.155 -3.597 -4.151 1.00 9.45 C
ATOM 33 CG GLU A 5 1.035 -4.713 -3.663 1.00 10.16 C
ATOM 34 CD GLU A 5 2.009 -5.243 -4.706 1.00 10.01 C
ATOM 35 OE1 GLU A 5 2.127 -4.680 -5.822 1.00 10.67 O
ATOM 36 OE2 GLU A 5 2.653 -6.260 -4.403 1.00 10.98 O
ATOM 37 N VAL A 6 1.129 -0.742 -5.983 1.00 13.27 N
ATOM 38 CA VAL A 6 0.694 0.201 -7.016 1.00 15.08 C
ATOM 39 C VAL A 6 1.239 -0.152 -8.414 1.00 16.11 C
ATOM 40 O VAL A 6 2.388 0.136 -8.755 1.00 17.57 O
ATOM 41 CB VAL A 6 1.089 1.654 -6.625 1.00 15.51 C
ATOM 42 CG1 VAL A 6 0.230 2.140 -5.472 1.00 15.79 C
ATOM 43 CG2 VAL A 6 2.539 1.722 -6.216 1.00 16.27 C
ATOM 44 OXT VAL A 6 0.534 -0.718 -9.323 1.00 17.23 O
TER 45 VAL A 6
HETATM 46 O HOH A 7 -1.258 -3.852 6.869 1.00 20.35 O
HETATM 47 O HOH A 8 -2.085 3.217 8.261 1.00 30.60 O
MASTER 244 0 0 0 0 0 0 6 46 1 0 1
END