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