HEADER PROTEIN FIBRIL 15-JUN-11 3SGN TITLE BROMODERIVATIVE-8 OF AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN TITLE 2 RESIDUES 90-100 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-CRYSTALLIN B CHAIN; COMPND 3 CHAIN: A, B; 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 OLIGOMER, BETA CYLINDRIN, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR A.LAGANOWSKY,M.R.SAWAYA,D.CASCIO,D.EISENBERG REVDAT 1 21-MAR-12 3SGN 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. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 1473 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.180 REMARK 3 FREE R VALUE TEST SET COUNT : 150 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 35.1737 - 2.8070 0.98 1323 150 0.2103 0.2272 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 : 0.29 REMARK 3 B_SOL : 46.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.740 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.560 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) : -0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.00000 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 : 0.011 168 REMARK 3 ANGLE : 1.579 224 REMARK 3 CHIRALITY : 0.070 32 REMARK 3 PLANARITY : 0.004 26 REMARK 3 DIHEDRAL : 20.298 62 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 3SGN 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 RCSB ID CODE IS RCSB066178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.91963 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 : 2765 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 30% MPD, 0.2M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 35.17100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 35.17100 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 35.17100 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 35.17100 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 35.17100 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 35.17100 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 BIOMT1 2 0.000000 0.000000 1.000000 35.17100 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 105.51300 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 70.34200 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 105.51300 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 70.34200 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 -35.17100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SGM RELATED DB: PDB REMARK 900 BROMODERIVATIVE-2 OF AMYLOID-RELATED SEGMENT OF ALPHAB- REMARK 900 CRYSTALLIN 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- REMARK 900 100 MUTANT V91L REMARK 900 RELATED ID: 3SGR RELATED DB: PDB REMARK 900 TANDEM REPEAT OF AMYLOID-RELATED SEGMENT OF ALPHAB- REMARK 900 CRYSTALLIN RESIDUES 90-100 MUTANT V91L REMARK 900 RELATED ID: 3SGS RELATED DB: PDB REMARK 900 AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN RESIDUES 95-100 DBREF 3SGN A 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 3SGN B 1 11 UNP P02511 CRYAB_HUMAN 90 100 SEQRES 1 A 11 LYS VAL LYS VAL LEU GLY ASP A8E ILE GLU VAL SEQRES 1 B 11 LYS VAL LYS VAL LEU GLY ASP A8E ILE GLU VAL MODRES 3SGN A8E A 8 VAL (2S)-2-AMINO-4-BROMOPENT-4-ENOIC ACID MODRES 3SGN A8E B 8 VAL (2S)-2-AMINO-4-BROMOPENT-4-ENOIC ACID HET A8E A 8 8 HET A8E B 8 8 HETNAM A8E (2S)-2-AMINO-4-BROMOPENT-4-ENOIC ACID FORMUL 1 A8E 2(C5 H8 BR N O2) FORMUL 3 HOH *2(H2 O) SHEET 1 A 2 VAL A 2 GLU A 10 0 SHEET 2 A 2 VAL B 2 GLU B 10 -1 O LEU B 5 N ASP A 7 LINK C A8E A 8 N ILE A 9 1555 1555 1.33 LINK C A8E B 8 N ILE B 9 1555 1555 1.33 CRYST1 70.342 70.342 70.342 90.00 90.00 90.00 I 21 3 48 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 0.014216 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014216 0.00000