HEADER STRUCTURAL PROTEIN 14-JUL-21 7P53 TITLE CRYSTAL STRUCTURE OF HUMAN GAMMA-D-CRYSTALLIN MUTANT C110M AT 1.57 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-CRYSTALLIN D; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: GAMMA-D-CRYSTALLIN,GAMMA-CRYSTALLIN 4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THE PROTEIN IS A MUTANT OF HUMAN GAMMA-D CRYSTALLIN COMPND 8 WHERE THE 110TH CYSTEINE IS REPLACED BY A METHIONINE (C110M). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: EYE; SOURCE 6 GENE: CRYGD, CRYG4; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: BL21-GOLD(DE3) KEYWDS CYSTEINE MUTATION, RECOMBINANT, STRUCTURAL PROTEIN, EYE LENS EXPDTA X-RAY DIFFRACTION AUTHOR A.STROFALDI,A.R.KHAN,J.MCMANUS REVDAT 2 31-JAN-24 7P53 1 REMARK REVDAT 1 13-OCT-21 7P53 0 JRNL AUTH A.STROFALDI,A.R.KHAN,J.J.MCMANUS JRNL TITL SURFACE EXPOSED FREE CYSTEINE SUPPRESSES CRYSTALLIZATION OF JRNL TITL 2 HUMAN GAMMA D-CRYSTALLIN. JRNL REF J.MOL.BIOL. V. 433 67252 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 34537240 JRNL DOI 10.1016/J.JMB.2021.167252 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 22423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1126 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 45.5100 - 3.1500 0.99 2877 150 0.1708 0.2204 REMARK 3 2 3.1500 - 2.5000 1.00 2768 136 0.2004 0.2612 REMARK 3 3 2.5000 - 2.1800 1.00 2706 149 0.2031 0.2538 REMARK 3 4 2.1800 - 1.9800 0.99 2676 132 0.2419 0.3438 REMARK 3 5 1.9800 - 1.8400 0.99 2693 140 0.2904 0.3695 REMARK 3 6 1.8400 - 1.7300 0.99 2661 142 0.3308 0.3321 REMARK 3 7 1.7300 - 1.6400 0.99 2651 157 0.3775 0.4692 REMARK 3 8 1.6400 - 1.5700 0.85 2265 120 0.4399 0.4318 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.562 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.55 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 : 0.010 1506 REMARK 3 ANGLE : 1.067 2029 REMARK 3 CHIRALITY : 0.059 191 REMARK 3 PLANARITY : 0.019 271 REMARK 3 DIHEDRAL : 14.159 570 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 7P53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292116704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 52.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.18800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 1.94100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.15.2_3472 REMARK 200 STARTING MODEL: 1HK0 REMARK 200 REMARK 200 REMARK: RHOMBIC CRYSTALS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED IN 0.1M SODIUM REMARK 280 PHOSPHATE BUFFER PH 7 INDUCING LLPS AT APPROXIMATELY 263K FOR REMARK 280 3HOURS FROM 150MG/ML SOLUTIONS. CRYSTALS WERE OBSERVED AFTER FEW REMARK 280 HOURS OF INCUBATION AT 277K., BATCH MODE 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 16.84950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.77700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.42200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.77700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.84950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.42200 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 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 X 24 87.86 -155.71 REMARK 500 LEU X 29 116.06 -162.00 REMARK 500 ARG X 116 59.45 -90.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG X 151 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7P53 X 1 173 UNP P07320 CRGD_HUMAN 2 174 SEQADV 7P53 MET X 110 UNP P07320 CYS 111 ENGINEERED MUTATION SEQRES 1 X 173 GLY LYS ILE THR LEU TYR GLU ASP ARG GLY PHE GLN GLY SEQRES 2 X 173 ARG HIS TYR GLU CYS SER SER ASP HIS PRO ASN LEU GLN SEQRES 3 X 173 PRO TYR LEU SER ARG CYS ASN SER ALA ARG VAL ASP SER SEQRES 4 X 173 GLY CYS TRP MET LEU TYR GLU GLN PRO ASN TYR SER GLY SEQRES 5 X 173 LEU GLN TYR PHE LEU ARG ARG GLY ASP TYR ALA ASP HIS SEQRES 6 X 173 GLN GLN TRP MET GLY LEU SER ASP SER VAL ARG SER CYS SEQRES 7 X 173 ARG LEU ILE PRO HIS SER GLY SER HIS ARG ILE ARG LEU SEQRES 8 X 173 TYR GLU ARG GLU ASP TYR ARG GLY GLN MET ILE GLU PHE SEQRES 9 X 173 THR GLU ASP CYS SER MET LEU GLN ASP ARG PHE ARG PHE SEQRES 10 X 173 ASN GLU ILE HIS SER LEU ASN VAL LEU GLU GLY SER TRP SEQRES 11 X 173 VAL LEU TYR GLU LEU SER ASN TYR ARG GLY ARG GLN TYR SEQRES 12 X 173 LEU LEU MET PRO GLY ASP TYR ARG ARG TYR GLN ASP TRP SEQRES 13 X 173 GLY ALA THR ASN ALA ARG VAL GLY SER LEU ARG ARG VAL SEQRES 14 X 173 ILE ASP PHE SER FORMUL 2 HOH *108(H2 O) HELIX 1 AA1 ARG X 9 PHE X 11 5 3 HELIX 2 AA2 ASP X 64 MET X 69 5 6 HELIX 3 AA3 ARG X 94 ARG X 98 5 5 HELIX 4 AA4 MET X 110 PHE X 115 1 6 HELIX 5 AA5 ARG X 152 GLY X 157 5 6 SHEET 1 AA1 4 GLN X 12 CYS X 18 0 SHEET 2 AA1 4 LYS X 2 ASP X 8 -1 N GLU X 7 O ARG X 14 SHEET 3 AA1 4 SER X 34 SER X 39 -1 O SER X 34 N TYR X 6 SHEET 4 AA1 4 GLY X 60 TYR X 62 -1 O GLY X 60 N VAL X 37 SHEET 1 AA2 3 SER X 51 LEU X 57 0 SHEET 2 AA2 3 CYS X 41 GLN X 47 -1 N TRP X 42 O LEU X 57 SHEET 3 AA2 3 SER X 77 ILE X 81 -1 O ARG X 79 N MET X 43 SHEET 1 AA3 4 MET X 101 PHE X 104 0 SHEET 2 AA3 4 ARG X 88 TYR X 92 -1 N LEU X 91 O ILE X 102 SHEET 3 AA3 4 SER X 122 GLU X 127 -1 O SER X 122 N TYR X 92 SHEET 4 AA3 4 GLY X 148 TYR X 150 -1 O TYR X 150 N LEU X 123 SHEET 1 AA4 3 ARG X 139 LEU X 145 0 SHEET 2 AA4 3 TRP X 130 LEU X 135 -1 N TRP X 130 O LEU X 145 SHEET 3 AA4 3 SER X 165 ARG X 168 -1 O ARG X 167 N VAL X 131 CRYST1 33.699 52.844 89.554 90.00 90.00 90.00 P 21 21 21 4 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 0.029674 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011166 0.00000