HEADER STRUCTURAL PROTEIN 30-SEP-22 8H0R TITLE CRYSTAL STRUCTURE OF A CATARACT-CAUSING CRYSTALLIN MUTANT (MOUSE TITLE 2 CRYBB1 Y202X) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-CRYSTALLIN B1B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CRYBB1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PROTEIN DEGRADATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CRYBB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS CRYSTALLIN CRYBB1, TRANCATED MUTANT, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.JING,P.GONG REVDAT 2 16-AUG-23 8H0R 1 JRNL REVDAT 1 05-JUL-23 8H0R 0 JRNL AUTH X.JING,M.ZHU,X.LU,P.WEI,L.SHI,B.Y.ZHANG,Y.XU,Y.P.TANG, JRNL AUTH 2 D.M.XIANG,P.GONG JRNL TITL CATARACT-CAUSING Y204X MUTATION OF CRYSTALLIN PROTEIN CRY JRNL TITL 2 BETA B1 PROMOTES ITS C-TERMINAL DEGRADATION AND HIGHER-ORDER JRNL TITL 3 OLIGOMERIZATION. JRNL REF J.BIOL.CHEM. V. 299 04953 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37356717 JRNL DOI 10.1016/J.JBC.2023.104953 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 68096 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3398 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 23.1030 - 3.4598 0.97 2894 133 0.1687 0.1832 REMARK 3 2 3.4598 - 2.7476 1.00 2830 162 0.1674 0.1674 REMARK 3 3 2.7476 - 2.4007 1.00 2806 141 0.1973 0.2052 REMARK 3 4 2.4007 - 2.1814 1.00 2797 141 0.1822 0.1712 REMARK 3 5 2.1814 - 2.0251 1.00 2779 118 0.1761 0.1832 REMARK 3 6 2.0251 - 1.9058 1.00 2744 153 0.1737 0.2019 REMARK 3 7 1.9058 - 1.8104 1.00 2754 162 0.1833 0.2115 REMARK 3 8 1.8104 - 1.7316 1.00 2736 148 0.1806 0.2039 REMARK 3 9 1.7316 - 1.6650 1.00 2743 147 0.1830 0.1741 REMARK 3 10 1.6650 - 1.6075 1.00 2750 138 0.1878 0.2094 REMARK 3 11 1.6075 - 1.5573 1.00 2719 161 0.1895 0.1788 REMARK 3 12 1.5573 - 1.5128 1.00 2744 145 0.1912 0.1914 REMARK 3 13 1.5128 - 1.4730 1.00 2708 148 0.1943 0.2077 REMARK 3 14 1.4730 - 1.4370 1.00 2724 153 0.1925 0.2142 REMARK 3 15 1.4370 - 1.4044 1.00 2740 151 0.2034 0.2350 REMARK 3 16 1.4044 - 1.3745 1.00 2679 146 0.2083 0.2431 REMARK 3 17 1.3745 - 1.3470 1.00 2738 136 0.2124 0.2262 REMARK 3 18 1.3470 - 1.3216 1.00 2736 142 0.2154 0.2337 REMARK 3 19 1.3216 - 1.2980 1.00 2719 133 0.2185 0.2145 REMARK 3 20 1.2980 - 1.2760 0.99 2666 148 0.2262 0.2430 REMARK 3 21 1.2760 - 1.2554 0.98 2669 143 0.2347 0.2693 REMARK 3 22 1.2554 - 1.2361 0.93 2520 129 0.2398 0.2711 REMARK 3 23 1.2361 - 1.2179 0.87 2356 114 0.2594 0.2697 REMARK 3 24 1.2179 - 1.2010 0.79 2147 106 0.2664 0.3177 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.44 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 1554 REMARK 3 ANGLE : 0.890 2105 REMARK 3 CHIRALITY : 0.093 209 REMARK 3 PLANARITY : 0.005 277 REMARK 3 DIHEDRAL : 12.159 924 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 8H0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 06-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300022662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68183 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 6.0, EVAPORATION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 19.95950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.66050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.21850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.66050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.95950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.21850 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO B 53 REMARK 465 PRO B 54 REMARK 465 GLY B 55 REMARK 465 ASP B 87 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 141 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 88 CG CD NE CZ NH1 NH2 REMARK 470 MET B 142 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN B 80 101.35 -163.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 8H0R A 53 143 UNP Q9WVJ5 CRBB1_MOUSE 53 143 DBREF 8H0R B 53 143 UNP Q9WVJ5 CRBB1_MOUSE 53 143 SEQRES 1 A 91 PRO PRO GLY SER TYR ARG LEU ILE VAL PHE GLU GLN GLU SEQRES 2 A 91 ASN PHE GLN GLY ARG ARG VAL GLU PHE SER GLY GLU CYS SEQRES 3 A 91 LEU ASN LEU GLY ASP ARG GLY PHE ASP ARG VAL ARG SER SEQRES 4 A 91 LEU ILE VAL VAL SER GLY PRO TRP VAL ALA PHE GLU GLN SEQRES 5 A 91 SER ALA PHE ARG GLY GLU MET PHE VAL LEU GLU LYS GLY SEQRES 6 A 91 GLU TYR PRO ARG TRP ASP THR TRP THR SER SER TYR ARG SEQRES 7 A 91 SER ASP ARG LEU MET SER PHE ARG PRO ILE ARG MET ASP SEQRES 1 B 91 PRO PRO GLY SER TYR ARG LEU ILE VAL PHE GLU GLN GLU SEQRES 2 B 91 ASN PHE GLN GLY ARG ARG VAL GLU PHE SER GLY GLU CYS SEQRES 3 B 91 LEU ASN LEU GLY ASP ARG GLY PHE ASP ARG VAL ARG SER SEQRES 4 B 91 LEU ILE VAL VAL SER GLY PRO TRP VAL ALA PHE GLU GLN SEQRES 5 B 91 SER ALA PHE ARG GLY GLU MET PHE VAL LEU GLU LYS GLY SEQRES 6 B 91 GLU TYR PRO ARG TRP ASP THR TRP THR SER SER TYR ARG SEQRES 7 B 91 SER ASP ARG LEU MET SER PHE ARG PRO ILE ARG MET ASP FORMUL 3 HOH *187(H2 O) HELIX 1 AA1 GLN A 64 GLN A 68 5 5 HELIX 2 AA2 ASN A 80 GLY A 85 5 6 HELIX 3 AA3 ARG A 121 TRP A 125 5 5 HELIX 4 AA4 ASN B 80 GLY B 85 5 6 HELIX 5 AA5 SER B 105 PHE B 107 5 3 HELIX 6 AA6 ARG B 121 TRP B 125 5 5 SHEET 1 AA1 4 ARG A 71 PHE A 74 0 SHEET 2 AA1 4 ARG A 58 PHE A 62 -1 N LEU A 59 O PHE A 74 SHEET 3 AA1 4 SER A 91 SER A 96 -1 O ILE A 93 N ILE A 60 SHEET 4 AA1 4 GLY A 117 TYR A 119 -1 O GLY A 117 N VAL A 94 SHEET 1 AA2 3 ARG A 108 LEU A 114 0 SHEET 2 AA2 3 TRP A 99 GLN A 104 -1 N TRP A 99 O LEU A 114 SHEET 3 AA2 3 SER A 136 PRO A 139 -1 O SER A 136 N PHE A 102 SHEET 1 AA3 4 GLN B 68 PHE B 74 0 SHEET 2 AA3 4 ARG B 58 GLN B 64 -1 N LEU B 59 O PHE B 74 SHEET 3 AA3 4 SER B 91 SER B 96 -1 O ILE B 93 N ILE B 60 SHEET 4 AA3 4 GLY B 117 TYR B 119 -1 O GLY B 117 N VAL B 94 SHEET 1 AA4 3 ARG B 108 LEU B 114 0 SHEET 2 AA4 3 TRP B 99 GLN B 104 -1 N TRP B 99 O LEU B 114 SHEET 3 AA4 3 SER B 136 PRO B 139 -1 O ARG B 138 N VAL B 100 CISPEP 1 GLY A 97 PRO A 98 0 3.41 CISPEP 2 GLY B 97 PRO B 98 0 2.46 CRYST1 39.919 48.437 113.321 90.00 90.00 90.00 P 21 21 21 8 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 0.025051 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008824 0.00000