HEADER PROTEIN FIBRIL 30-JUL-21 7ROJ TITLE AMYLOID-RELATED SEGMENT OF ALPHAB-CRYSTALLIN RESIDUES 90-100 WITH G95W TITLE 2 MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-CRYSTALLIN B CHAIN PEPTIDE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L; COMPND 4 FRAGMENT: RESIDUES 90-100; COMPND 5 SYNONYM: ALPHA(B)-CRYSTALLIN,HEAT SHOCK PROTEIN BETA-5,HSPB5,RENAL COMPND 6 CARCINOMA ANTIGEN NY-REN-27,ROSENTHAL FIBER COMPONENT; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 KEYWDS AMYLOID OLIGOMER, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,T.D.DO,D.S.EISENBERG REVDAT 3 18-OCT-23 7ROJ 1 REMARK REVDAT 2 02-MAR-22 7ROJ 1 JRNL REVDAT 1 12-JAN-22 7ROJ 0 JRNL AUTH A.L.H.GRAY,M.R.SAWAYA,D.ACHARYYA,J.LOU,E.M.EDINGTON, JRNL AUTH 2 M.D.BEST,R.A.PROSSER,D.S.EISENBERG,T.D.DO JRNL TITL ATOMIC VIEW OF AN AMYLOID DODECAMER EXHIBITING SELECTIVE JRNL TITL 2 CELLULAR TOXIC VULNERABILITY IN ACUTE BRAIN SLICES. JRNL REF PROTEIN SCI. V. 31 716 2022 JRNL REFN ESSN 1469-896X JRNL PMID 34954854 JRNL DOI 10.1002/PRO.4268 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 14353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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 64.0900 - 3.4500 0.90 1304 145 0.1902 0.2422 REMARK 3 2 3.4500 - 2.7400 0.95 1332 148 0.2244 0.2336 REMARK 3 3 2.7400 - 2.3900 0.92 1287 143 0.2591 0.2863 REMARK 3 4 2.3900 - 2.1700 0.94 1331 148 0.2498 0.2874 REMARK 3 5 2.1700 - 2.0200 0.94 1289 144 0.2676 0.3181 REMARK 3 6 2.0200 - 1.9000 0.92 1297 144 0.2773 0.3161 REMARK 3 7 1.9000 - 1.8000 0.94 1292 144 0.2982 0.3422 REMARK 3 8 1.8000 - 1.7200 0.86 1216 134 0.3370 0.4028 REMARK 3 9 1.7200 - 1.6600 0.92 1279 142 0.3472 0.4178 REMARK 3 10 1.6600 - 1.6000 0.94 1290 144 0.3685 0.3793 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.262 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.972 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.006 1180 REMARK 3 ANGLE : 0.890 1604 REMARK 3 CHIRALITY : 0.063 205 REMARK 3 PLANARITY : 0.005 174 REMARK 3 DIHEDRAL : 14.798 420 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.0384 -1.6084 16.1600 REMARK 3 T TENSOR REMARK 3 T11: 0.1542 T22: 0.1617 REMARK 3 T33: 0.1672 T12: 0.0048 REMARK 3 T13: -0.0082 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.9440 L22: 0.5049 REMARK 3 L33: 0.5283 L12: 0.5398 REMARK 3 L13: -0.0528 L23: 0.0847 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.0903 S13: -0.0033 REMARK 3 S21: -0.0193 S22: 0.0078 S23: 0.1032 REMARK 3 S31: -0.0102 S32: 0.0431 S33: 0.0013 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 7ROJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-20 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) : 0.97918 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14376 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 64.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 2.042 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1400 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) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.05 REMARK 200 R MERGE FOR SHELL (I) : 0.91600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 7ROL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1,4-BUTANEDIOL, HEPES, NACL, REMARK 280 TRIFLUOROACETIC ACID, GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 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 18.16500 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 10 OE1 REMARK 620 2 GLU K 10 OE2 90.2 REMARK 620 3 VAL K 11 O 163.4 89.5 REMARK 620 N 1 2 DBREF 7ROJ A 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ B 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ C 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ D 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ E 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ F 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ G 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ H 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ I 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ J 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ K 1 11 UNP P02511 CRYAB_HUMAN 90 100 DBREF 7ROJ L 1 11 UNP P02511 CRYAB_HUMAN 90 100 SEQADV 7ROJ TRP A 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP B 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP C 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP D 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP E 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP F 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP G 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP H 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP I 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP J 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP K 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQADV 7ROJ TRP L 6 UNP P02511 GLY 95 ENGINEERED MUTATION SEQRES 1 A 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 B 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 C 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 D 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 E 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 F 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 G 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 H 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 I 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 J 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 K 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL SEQRES 1 L 11 LYS VAL LYS VAL LEU TRP ASP VAL ILE GLU VAL HET NA A 101 1 HET TFA B 101 7 HET TFA C 101 7 HET TFA G 101 7 HET GOL I 101 12 HET TFA K 101 7 HETNAM NA SODIUM ION HETNAM TFA TRIFLUOROACETIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 13 NA NA 1+ FORMUL 14 TFA 4(C2 H F3 O2) FORMUL 17 GOL C3 H8 O3 FORMUL 19 HOH *38(H2 O) SHEET 1 AA1 4 VAL A 2 GLU A 10 0 SHEET 2 AA1 4 VAL B 2 GLU B 10 -1 O LEU B 5 N ASP A 7 SHEET 3 AA1 4 VAL D 2 GLU D 10 -1 O VAL D 4 N TRP B 6 SHEET 4 AA1 4 VAL C 2 GLU C 10 -1 N ASP C 7 O LEU D 5 SHEET 1 AA2 4 VAL F 2 GLU F 10 0 SHEET 2 AA2 4 VAL E 2 GLU E 10 -1 N LYS E 3 O ILE F 9 SHEET 3 AA2 4 VAL K 2 ILE K 9 -1 O VAL K 4 N TRP E 6 SHEET 4 AA2 4 LYS L 3 GLU L 10 -1 O LEU L 5 N ASP K 7 SHEET 1 AA3 4 VAL H 2 GLU H 10 0 SHEET 2 AA3 4 VAL G 2 GLU G 10 -1 N ASP G 7 O LEU H 5 SHEET 3 AA3 4 VAL J 2 GLU J 10 -1 O VAL J 4 N TRP G 6 SHEET 4 AA3 4 VAL I 2 GLU I 10 -1 N LEU I 5 O ASP J 7 LINK OE1 GLU A 10 NA NA A 101 1555 1555 2.30 LINK NA NA A 101 OE2 GLU K 10 1555 1555 2.55 LINK NA NA A 101 O VAL K 11 1555 1555 2.45 CRYST1 25.270 36.330 64.130 90.00 91.92 90.00 P 1 21 1 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 0.039573 0.000000 0.001327 0.00000 SCALE2 0.000000 0.027525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015602 0.00000