HEADER PROTEIN FIBRIL 04-MAR-12 4E0K TITLE CRYSTAL STRUCTURE OF THE AMYLOID-FIBRIL FORMING PEPTIDE KDWSFY DERIVED TITLE 2 FROM HUMAN BETA 2 MICROGLOBULIN (58-63) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOIDOGENIC PEPTIDE SEGMENT KDWSFY; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS AMYLOID, OUT-OF-REGISTER, FIBER-FORMING, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHAO,C.LIU,M.R.SAWAYA,D.EISENBERG REVDAT 3 28-FEB-24 4E0K 1 REMARK REVDAT 2 19-JUN-13 4E0K 1 JRNL REVDAT 1 19-DEC-12 4E0K 0 JRNL AUTH C.LIU,M.ZHAO,L.JIANG,P.N.CHENG,J.PARK,M.R.SAWAYA, JRNL AUTH 2 A.PENSALFINI,D.GOU,A.J.BERK,C.G.GLABE,J.NOWICK,D.EISENBERG JRNL TITL OUT-OF-REGISTER BETA-SHEETS SUGGEST A PATHWAY TO TOXIC JRNL TITL 2 AMYLOID AGGREGATES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 20913 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23213214 JRNL DOI 10.1073/PNAS.1218792109 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.112 REMARK 3 FREE R VALUE : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1601 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 14.9826 - 2.1559 0.99 1393 156 0.1304 0.1445 REMARK 3 2 2.1559 - 1.7120 1.00 1330 147 0.1075 0.1349 REMARK 3 3 1.7120 - 1.4958 1.00 1320 147 0.1003 0.1325 REMARK 3 4 1.4958 - 1.3592 1.00 1314 146 0.0982 0.1029 REMARK 3 5 1.3592 - 1.2618 1.00 1316 146 0.0961 0.1238 REMARK 3 6 1.2618 - 1.1874 1.00 1291 144 0.0941 0.1198 REMARK 3 7 1.1874 - 1.1280 1.00 1299 144 0.0891 0.1048 REMARK 3 8 1.1280 - 1.0789 1.00 1278 142 0.0908 0.1088 REMARK 3 9 1.0789 - 1.0374 1.00 1301 145 0.1072 0.1138 REMARK 3 10 1.0374 - 1.0016 1.00 1303 144 0.1342 0.1571 REMARK 3 11 1.0016 - 0.9703 0.99 1251 140 0.1495 0.1713 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.77 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 38.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22070 REMARK 3 B22 (A**2) : 0.22070 REMARK 3 B33 (A**2) : -0.44150 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.010 369 REMARK 3 ANGLE : 1.417 495 REMARK 3 CHIRALITY : 0.095 37 REMARK 3 PLANARITY : 0.009 58 REMARK 3 DIHEDRAL : 19.613 163 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 4E0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 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 : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 14.981 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH 6.5, 0.2 M REMARK 280 SODIUM FLUORIDE, 20% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 3.91000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.82000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.86500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.77500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 1.95500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PE4 B 101 REMARK 610 PE4 C 101 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE4 C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E0L RELATED DB: PDB REMARK 900 RELATED ID: 4E0M RELATED DB: PDB REMARK 900 RELATED ID: 4E0N RELATED DB: PDB REMARK 900 RELATED ID: 4E0O RELATED DB: PDB DBREF 4E0K A 1 6 PDB 4E0K 4E0K 1 6 DBREF 4E0K B 1 6 PDB 4E0K 4E0K 1 6 DBREF 4E0K C 1 6 PDB 4E0K 4E0K 1 6 DBREF 4E0K D 1 6 PDB 4E0K 4E0K 1 6 SEQRES 1 A 6 LYS ASP TRP SER PHE TYR SEQRES 1 B 6 LYS ASP TRP SER PHE TYR SEQRES 1 C 6 LYS ASP TRP SER PHE TYR SEQRES 1 D 6 LYS ASP TRP SER PHE TYR HET PE4 B 101 30 HET NA B 102 1 HET PE4 C 101 15 HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETNAM NA SODIUM ION HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 FORMUL 5 PE4 2(C16 H34 O8) FORMUL 6 NA NA 1+ FORMUL 8 HOH *49(H2 O) SHEET 1 A 2 ASP A 2 PHE A 5 0 SHEET 2 A 2 TRP B 3 TYR B 6 -1 O TYR B 6 N ASP A 2 SHEET 1 B 2 TRP C 3 PHE C 5 0 SHEET 2 B 2 TRP D 3 PHE D 5 -1 O SER D 4 N SER C 4 LINK OD1BASP B 2 NA NA B 102 1555 1555 2.83 SITE 1 AC1 12 TRP A 3 TYR A 6 HOH A 103 TRP B 3 SITE 2 AC1 12 PHE B 5 TYR B 6 HOH B 203 HOH B 207 SITE 3 AC1 12 HOH B 208 TRP C 3 TRP D 3 PHE D 5 SITE 1 AC2 5 PHE A 5 ASP B 2 TRP B 3 LYS D 1 SITE 2 AC2 5 HOH D 109 SITE 1 AC3 3 TYR C 6 HOH C 206 TYR D 6 CRYST1 62.370 62.370 11.730 90.00 90.00 120.00 P 61 24 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 0.016033 0.009257 0.000000 0.00000 SCALE2 0.000000 0.018514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.085251 0.00000