HEADER STRUCTURAL PROTEIN 22-DEC-17 6FD8 TITLE GAMMA-S CRYSTALLIN DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-CRYSTALLIN S; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GAMMA-S-CRYSTALLIN,GAMMA-CRYSTALLIN S; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CRYGS, CRYG8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRYSTALLIN, EYE LENS, VISION, CATARACT., STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.D.MABBITT,D.C.THORN,C.J.JACKSON,J.A.CARVER REVDAT 4 17-JAN-24 6FD8 1 SSBOND REVDAT 3 06-FEB-19 6FD8 1 JRNL REMARK REVDAT 2 16-JAN-19 6FD8 1 REMARK REVDAT 1 26-DEC-18 6FD8 0 JRNL AUTH D.C.THORN,A.B.GROSAS,P.D.MABBITT,N.J.RAY,C.J.JACKSON, JRNL AUTH 2 J.A.CARVER JRNL TITL THE STRUCTURE AND STABILITY OF THE DISULFIDE-LINKED GAMMA JRNL TITL 2 S-CRYSTALLIN DIMER PROVIDE INSIGHT INTO OXIDATION PRODUCTS JRNL TITL 3 ASSOCIATED WITH LENS CATARACT FORMATION. JRNL REF J. MOL. BIOL. V. 431 483 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 30552875 JRNL DOI 10.1016/J.JMB.2018.12.005 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 23387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.460 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 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 43.1235 - 4.0163 0.95 3177 261 0.1591 0.2170 REMARK 3 2 4.0163 - 3.1882 0.91 3135 140 0.1957 0.2742 REMARK 3 3 3.1882 - 2.7852 0.95 3307 90 0.2416 0.2989 REMARK 3 4 2.7852 - 2.5306 0.94 3225 160 0.2784 0.3324 REMARK 3 5 2.5306 - 2.3492 0.94 3193 167 0.2884 0.3776 REMARK 3 6 2.3492 - 2.2107 0.88 3088 96 0.3746 0.4143 REMARK 3 7 2.2107 - 2.1000 0.94 3218 130 0.3213 0.3857 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.200 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) : 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 : 0.008 2978 REMARK 3 ANGLE : 0.943 4018 REMARK 3 CHIRALITY : 0.059 384 REMARK 3 PLANARITY : 0.006 526 REMARK 3 DIHEDRAL : 3.174 1752 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 6FD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23548 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 43.114 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 5VH1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM TARTRATE DIBASIC REMARK 280 DIHYDRATE (PH 7.3), 20% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 19.74574 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 23.45172 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -44.41958 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 MET A 0 REMARK 465 SER A 1 REMARK 465 LYS A 2 REMARK 465 THR A 3 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 LYS B 2 REMARK 465 THR B 3 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 CYS A 24 112.10 170.45 REMARK 500 ASP A 25 92.84 34.36 REMARK 500 ASP A 28 110.40 -162.75 REMARK 500 SER A 80 14.00 -145.77 REMARK 500 CYS A 82 145.08 -172.47 REMARK 500 PHE A 103 36.50 70.42 REMARK 500 LYS A 153 89.40 -56.10 REMARK 500 LYS A 154 -150.91 -150.47 REMARK 500 LYS B 6 -47.66 -132.86 REMARK 500 ASP B 25 109.27 51.17 REMARK 500 ASP B 28 106.81 -166.27 REMARK 500 SER B 80 -12.94 -140.04 REMARK 500 LYS B 154 -158.88 -160.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDEZ6 RELATED DB: SASBDB DBREF 6FD8 A 0 177 UNP P22914 CRBS_HUMAN 1 178 DBREF 6FD8 B 0 177 UNP P22914 CRBS_HUMAN 1 178 SEQRES 1 A 178 MET SER LYS THR GLY THR LYS ILE THR PHE TYR GLU ASP SEQRES 2 A 178 LYS ASN PHE GLN GLY ARG ARG TYR ASP CYS ASP CYS ASP SEQRES 3 A 178 CYS ALA ASP PHE HIS THR TYR LEU SER ARG CYS ASN SER SEQRES 4 A 178 ILE LYS VAL GLU GLY GLY THR TRP ALA VAL TYR GLU ARG SEQRES 5 A 178 PRO ASN PHE ALA GLY TYR MET TYR ILE LEU PRO GLN GLY SEQRES 6 A 178 GLU TYR PRO GLU TYR GLN ARG TRP MET GLY LEU ASN ASP SEQRES 7 A 178 ARG LEU SER SER CYS ARG ALA VAL HIS LEU PRO SER GLY SEQRES 8 A 178 GLY GLN TYR LYS ILE GLN ILE PHE GLU LYS GLY ASP PHE SEQRES 9 A 178 SER GLY GLN MET TYR GLU THR THR GLU ASP CYS PRO SER SEQRES 10 A 178 ILE MET GLU GLN PHE HIS MET ARG GLU ILE HIS SER CYS SEQRES 11 A 178 LYS VAL LEU GLU GLY VAL TRP ILE PHE TYR GLU LEU PRO SEQRES 12 A 178 ASN TYR ARG GLY ARG GLN TYR LEU LEU ASP LYS LYS GLU SEQRES 13 A 178 TYR ARG LYS PRO ILE ASP TRP GLY ALA ALA SER PRO ALA SEQRES 14 A 178 VAL GLN SER PHE ARG ARG ILE VAL GLU SEQRES 1 B 178 MET SER LYS THR GLY THR LYS ILE THR PHE TYR GLU ASP SEQRES 2 B 178 LYS ASN PHE GLN GLY ARG ARG TYR ASP CYS ASP CYS ASP SEQRES 3 B 178 CYS ALA ASP PHE HIS THR TYR LEU SER ARG CYS ASN SER SEQRES 4 B 178 ILE LYS VAL GLU GLY GLY THR TRP ALA VAL TYR GLU ARG SEQRES 5 B 178 PRO ASN PHE ALA GLY TYR MET TYR ILE LEU PRO GLN GLY SEQRES 6 B 178 GLU TYR PRO GLU TYR GLN ARG TRP MET GLY LEU ASN ASP SEQRES 7 B 178 ARG LEU SER SER CYS ARG ALA VAL HIS LEU PRO SER GLY SEQRES 8 B 178 GLY GLN TYR LYS ILE GLN ILE PHE GLU LYS GLY ASP PHE SEQRES 9 B 178 SER GLY GLN MET TYR GLU THR THR GLU ASP CYS PRO SER SEQRES 10 B 178 ILE MET GLU GLN PHE HIS MET ARG GLU ILE HIS SER CYS SEQRES 11 B 178 LYS VAL LEU GLU GLY VAL TRP ILE PHE TYR GLU LEU PRO SEQRES 12 B 178 ASN TYR ARG GLY ARG GLN TYR LEU LEU ASP LYS LYS GLU SEQRES 13 B 178 TYR ARG LYS PRO ILE ASP TRP GLY ALA ALA SER PRO ALA SEQRES 14 B 178 VAL GLN SER PHE ARG ARG ILE VAL GLU FORMUL 3 HOH *127(H2 O) HELIX 1 AA1 GLU A 68 MET A 73 5 6 HELIX 2 AA2 SER A 116 HIS A 122 1 7 HELIX 3 AA3 LYS A 158 TRP A 162 5 5 HELIX 4 AA4 ASP B 12 GLN B 16 5 5 HELIX 5 AA5 GLU B 68 MET B 73 5 6 HELIX 6 AA6 SER B 116 HIS B 122 1 7 HELIX 7 AA7 LYS B 158 GLY B 163 5 6 SHEET 1 AA1 4 GLN A 16 CYS A 22 0 SHEET 2 AA1 4 ILE A 7 ASP A 12 -1 N PHE A 9 O TYR A 20 SHEET 3 AA1 4 SER A 38 VAL A 41 -1 O SER A 38 N TYR A 10 SHEET 4 AA1 4 GLY A 64 TYR A 66 -1 O TYR A 66 N ILE A 39 SHEET 1 AA2 3 ALA A 55 LEU A 61 0 SHEET 2 AA2 3 TRP A 46 ARG A 51 -1 N ARG A 51 O ALA A 55 SHEET 3 AA2 3 SER A 81 ALA A 84 -1 O SER A 81 N TYR A 49 SHEET 1 AA3 4 SER A 104 THR A 110 0 SHEET 2 AA3 4 LYS A 94 LYS A 100 -1 N GLU A 99 O GLN A 106 SHEET 3 AA3 4 SER A 128 GLU A 133 -1 O GLU A 133 N LYS A 94 SHEET 4 AA3 4 GLU A 155 TYR A 156 -1 O TYR A 156 N CYS A 129 SHEET 1 AA4 3 GLN A 148 LEU A 151 0 SHEET 2 AA4 3 TRP A 136 TYR A 139 -1 N TRP A 136 O LEU A 151 SHEET 3 AA4 3 SER A 171 ARG A 174 -1 O SER A 171 N TYR A 139 SHEET 1 AA5 4 ARG B 19 CYS B 22 0 SHEET 2 AA5 4 ILE B 7 TYR B 10 -1 N PHE B 9 O TYR B 20 SHEET 3 AA5 4 SER B 38 VAL B 41 -1 O LYS B 40 N THR B 8 SHEET 4 AA5 4 GLY B 64 TYR B 66 -1 O GLY B 64 N VAL B 41 SHEET 1 AA6 3 ALA B 55 LEU B 61 0 SHEET 2 AA6 3 TRP B 46 ARG B 51 -1 N ARG B 51 O ALA B 55 SHEET 3 AA6 3 SER B 81 ALA B 84 -1 O SER B 81 N TYR B 49 SHEET 1 AA7 4 SER B 104 THR B 110 0 SHEET 2 AA7 4 LYS B 94 LYS B 100 -1 N GLU B 99 O GLN B 106 SHEET 3 AA7 4 SER B 128 GLU B 133 -1 O SER B 128 N PHE B 98 SHEET 4 AA7 4 GLU B 155 TYR B 156 -1 O TYR B 156 N CYS B 129 SHEET 1 AA8 3 ARG B 145 LEU B 151 0 SHEET 2 AA8 3 TRP B 136 LEU B 141 -1 N PHE B 138 O TYR B 149 SHEET 3 AA8 3 SER B 171 ARG B 174 -1 O SER B 171 N TYR B 139 SSBOND 1 CYS A 22 CYS A 26 1555 1555 2.04 SSBOND 2 CYS A 24 CYS B 24 1555 1554 2.03 SSBOND 3 CYS B 22 CYS B 26 1555 1555 2.04 CRYST1 49.632 52.365 53.972 108.72 111.46 105.50 P 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 0.020148 0.005587 0.011903 0.00000 SCALE2 0.000000 0.019817 0.010459 0.00000 SCALE3 0.000000 0.000000 0.022511 0.00000