HEADER DE NOVO PROTEIN, MEMBRANE PROTEIN 09-OCT-15 5E5X
TITLE STRUCTURE OF THE AMYLOID FORMING PEPTIDE ANFLVH (RESIDUES 13-18) FROM
TITLE 2 ISLET AMYLOID POLYPEPTIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ANFLVH (RESIDUES 13-18) FROM ISLET AMYLOID POLYPEPTIDE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS AMYLOID PROTO-FIBRIL, PROTEIN FIBRIL, DE NOVO PROTEIN, MEMBRANE
KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR A.B.SORIAGA,D.EISENBERG
REVDAT 4 06-MAR-24 5E5X 1 JRNL REMARK
REVDAT 3 20-JUL-16 5E5X 1 JRNL
REVDAT 2 20-JAN-16 5E5X 1 JRNL
REVDAT 1 16-DEC-15 5E5X 0
JRNL AUTH A.B.SORIAGA,S.SANGWAN,R.MACDONALD,M.R.SAWAYA,D.EISENBERG
JRNL TITL CRYSTAL STRUCTURES OF IAPP AMYLOIDOGENIC SEGMENTS REVEAL A
JRNL TITL 2 NOVEL PACKING MOTIF OF OUT-OF-REGISTER BETA SHEETS.
JRNL REF J.PHYS.CHEM.B V. 120 5810 2016
JRNL REFN ISSN 1089-5647
JRNL PMID 26629790
JRNL DOI 10.1021/ACS.JPCB.5B09981
REMARK 2
REMARK 2 RESOLUTION. 1.61 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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 : LS_WUNIT_K1
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3
REMARK 3 NUMBER OF REFLECTIONS : 433
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.118
REMARK 3 R VALUE (WORKING SET) : 0.113
REMARK 3 FREE R VALUE : 0.161
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160
REMARK 3 FREE R VALUE TEST SET COUNT : 44
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 19.8645 - 1.6101 0.93 389 44 0.1127 0.1612
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.00
REMARK 3 B_SOL : 0.00
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.290
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.450
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.65850
REMARK 3 B22 (A**2) : -3.01090
REMARK 3 B33 (A**2) : 2.35240
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.46120
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 : 0.003 51
REMARK 3 ANGLE : 0.704 69
REMARK 3 CHIRALITY : 0.058 8
REMARK 3 PLANARITY : 0.003 9
REMARK 3 DIHEDRAL : 16.988 15
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 5E5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15.
REMARK 100 THE DEPOSITION ID IS D_1000214419.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-NOV-09
REMARK 200 TEMPERATURE (KELVIN) : 291
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
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) : 0.979
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 : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 433
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
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 (%) : 93.3
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : 0.14700
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 6.5500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72
REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 9.700
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 (%): 6.32
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML IN WATER AND MIXED WITH 10%
REMARK 280 (W/V) PEG-8000, 0.1 M NA/K PHOSPHATE PH 6.2, AND 0.2 M NACL,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 19.86300
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 DISPLAYS ONLY A PORTION OF THE CRYSTAL
REMARK 300 LATTICE TO DEMONSTRATE THE CRYSTAL PACKING CONTENT. THE CRYSTAL
REMARK 300 PACKING IS FORMED BY A REPETITION IN BOTH DIRECTIONS OF THE PORTION
REMARK 300 INDICATED IN REMARK 350.
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 -14.49300
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 -9.66200
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 -4.83100
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 4.83100
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 -11.99768
REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 9.58863
REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 -7.16668
REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 9.58863
REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 -2.33568
REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 9.58863
REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 2.49532
REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 9.58863
REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 7.32632
REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 9.58863
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5E5V RELATED DB: PDB
REMARK 900 RELATED ID: 5E5Z RELATED DB: PDB
REMARK 900 RELATED ID: 5E61 RELATED DB: PDB
DBREF 5E5X A 1 6 PDB 5E5X 5E5X 1 6
SEQRES 1 A 6 ALA ASN PHE LEU VAL HIS
CRYST1 4.831 39.726 9.869 90.00 103.69 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 0.206996 0.000000 0.050418 0.00000
SCALE2 0.000000 0.025172 0.000000 0.00000
SCALE3 0.000000 0.000000 0.104290 0.00000
ATOM 1 N ALA A 1 0.863 -16.161 -1.139 1.00 7.31 N
ATOM 2 CA ALA A 1 1.590 -14.896 -1.111 1.00 6.67 C
ATOM 3 C ALA A 1 0.909 -13.893 -0.182 1.00 7.10 C
ATOM 4 O ALA A 1 -0.318 -13.853 -0.097 1.00 7.27 O
ATOM 5 CB ALA A 1 1.702 -14.324 -2.515 1.00 8.77 C
ATOM 6 N ASN A 2 1.716 -13.092 0.509 1.00 5.34 N
ATOM 7 CA ASN A 2 1.221 -12.023 1.380 1.00 6.89 C
ATOM 8 C ASN A 2 1.692 -10.661 0.876 1.00 7.36 C
ATOM 9 O ASN A 2 2.882 -10.476 0.627 1.00 6.23 O
ATOM 10 CB ASN A 2 1.720 -12.219 2.815 1.00 6.49 C
ATOM 11 CG ASN A 2 1.097 -13.420 3.495 1.00 7.48 C
ATOM 12 OD1 ASN A 2 -0.124 -13.574 3.516 1.00 7.39 O
ATOM 13 ND2 ASN A 2 1.935 -14.273 4.071 1.00 5.90 N
ATOM 14 N PHE A 3 0.761 -9.718 0.723 1.00 6.29 N
ATOM 15 CA PHE A 3 1.092 -8.357 0.293 1.00 6.89 C
ATOM 16 C PHE A 3 0.615 -7.335 1.322 1.00 6.80 C
ATOM 17 O PHE A 3 -0.564 -7.308 1.675 1.00 6.63 O
ATOM 18 CB PHE A 3 0.421 -8.017 -1.043 1.00 7.62 C
ATOM 19 CG PHE A 3 0.808 -8.919 -2.188 1.00 8.86 C
ATOM 20 CD1 PHE A 3 1.753 -8.514 -3.120 1.00 11.35 C
ATOM 21 CD2 PHE A 3 0.190 -10.150 -2.361 1.00 9.12 C
ATOM 22 CE1 PHE A 3 2.093 -9.334 -4.190 1.00 11.42 C
ATOM 23 CE2 PHE A 3 0.530 -10.974 -3.425 1.00 9.22 C
ATOM 24 CZ PHE A 3 1.479 -10.564 -4.340 1.00 10.39 C
ATOM 25 N LEU A 4 1.529 -6.489 1.792 1.00 5.88 N
ATOM 26 CA LEU A 4 1.167 -5.391 2.681 1.00 6.58 C
ATOM 27 C LEU A 4 1.774 -4.093 2.165 1.00 7.01 C
ATOM 28 O LEU A 4 2.995 -3.946 2.121 1.00 7.15 O
ATOM 29 CB LEU A 4 1.639 -5.664 4.113 1.00 5.66 C
ATOM 30 CG LEU A 4 1.062 -4.770 5.217 1.00 7.19 C
ATOM 31 CD1 LEU A 4 1.511 -5.269 6.582 1.00 9.46 C
ATOM 32 CD2 LEU A 4 1.457 -3.318 5.034 1.00 9.30 C
ATOM 33 N VAL A 5 0.915 -3.157 1.768 1.00 6.35 N
ATOM 34 CA VAL A 5 1.362 -1.830 1.356 1.00 6.65 C
ATOM 35 C VAL A 5 0.861 -0.787 2.352 1.00 7.02 C
ATOM 36 O VAL A 5 -0.341 -0.585 2.512 1.00 8.22 O
ATOM 37 CB VAL A 5 0.892 -1.474 -0.068 1.00 6.15 C
ATOM 38 CG1 VAL A 5 1.384 -0.091 -0.456 1.00 8.02 C
ATOM 39 CG2 VAL A 5 1.395 -2.510 -1.057 1.00 7.94 C
ATOM 40 N HIS A 6 1.805 -0.139 3.023 1.00 8.01 N
ATOM 41 CA HIS A 6 1.521 0.818 4.087 1.00 8.07 C
ATOM 42 C HIS A 6 1.151 2.188 3.522 1.00 10.79 C
ATOM 43 O HIS A 6 0.519 3.006 4.196 1.00 10.24 O
ATOM 44 CB HIS A 6 2.751 0.921 4.988 1.00 8.42 C
ATOM 45 CG HIS A 6 2.595 1.856 6.147 1.00 8.74 C
ATOM 46 ND1 HIS A 6 3.475 2.889 6.387 1.00 8.85 N
ATOM 47 CD2 HIS A 6 1.682 1.899 7.146 1.00 7.88 C
ATOM 48 CE1 HIS A 6 3.107 3.536 7.480 1.00 8.43 C
ATOM 49 NE2 HIS A 6 2.020 2.953 7.960 1.00 9.49 N
ATOM 50 OXT HIS A 6 1.474 2.513 2.376 1.00 9.27 O
TER 51 HIS A 6
MASTER 216 0 0 0 0 0 0 6 50 1 0 1
END