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