HEADER OXIDOREDUCTASE 29-JAN-21 7NCV TITLE CRYSTAL STRUCTURE OF REDUCED GLUTAREDOXIN 2 FROM CHLAMYDOMONAS TITLE 2 REINHARDTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN, CPYC TYPE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CYS56 RESIDUE IS OXIDIZED INTO A SULFENIC ACID. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 GENE: GRX2, CHLRE_12G550400V5, CHLREDRAFT_195611; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CHLAMYDOMONAS REINHARDTII GLUTAREDOXIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.RORET,C.DIDIERJEAN REVDAT 3 31-JAN-24 7NCV 1 JRNL REVDAT 2 16-JUN-21 7NCV 1 JRNL REVDAT 1 26-MAY-21 7NCV 0 JRNL AUTH T.RORET,B.ZHANG,A.MOSELER,T.DHALLEINE,X.H.GAO,J.COUTURIER, JRNL AUTH 2 S.D.LEMAIRE,C.DIDIERJEAN,M.K.JOHNSON,N.ROUHIER JRNL TITL ATYPICAL IRON-SULFUR CLUSTER BINDING, REDOX ACTIVITY AND JRNL TITL 2 STRUCTURAL PROPERTIES OF CHLAMYDOMONAS REINHARDTII JRNL TITL 3 GLUTAREDOXIN 2. JRNL REF ANTIOXIDANTS (BASEL) V. 10 2021 JRNL REFN ESSN 2076-3921 JRNL PMID 34069657 JRNL DOI 10.3390/ANTIOX10050803 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1070 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 39.5300 - 3.0000 0.97 2599 125 0.1539 0.1885 REMARK 3 2 3.0000 - 2.3800 1.00 2505 136 0.1606 0.1710 REMARK 3 3 2.3800 - 2.0800 1.00 2465 133 0.1415 0.1707 REMARK 3 4 2.0800 - 1.8900 1.00 2487 134 0.1375 0.1568 REMARK 3 5 1.8900 - 1.7600 1.00 2419 131 0.1354 0.1705 REMARK 3 6 1.7600 - 1.6500 1.00 2463 128 0.1555 0.1862 REMARK 3 7 1.6500 - 1.5700 1.00 2431 132 0.1688 0.2109 REMARK 3 8 1.5700 - 1.5000 0.98 2399 151 0.1980 0.2277 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) : 0.103 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.95 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 : 0.015 827 REMARK 3 ANGLE : 1.369 1115 REMARK 3 CHIRALITY : 0.088 127 REMARK 3 PLANARITY : 0.009 148 REMARK 3 DIHEDRAL : 22.124 308 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 107) REMARK 3 ORIGIN FOR THE GROUP (A): -15.4628 -13.1805 7.4253 REMARK 3 T TENSOR REMARK 3 T11: 0.1554 T22: 0.1588 REMARK 3 T33: 0.1525 T12: 0.0396 REMARK 3 T13: -0.0212 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.9186 L22: 0.9980 REMARK 3 L33: 2.2103 L12: 0.0449 REMARK 3 L13: 0.0418 L23: -0.0375 REMARK 3 S TENSOR REMARK 3 S11: -0.1084 S12: -0.0583 S13: 0.1291 REMARK 3 S21: -0.0274 S22: -0.0250 S23: 0.0152 REMARK 3 S31: -0.2947 S32: -0.1476 S33: -0.0070 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 7NCV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-12 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 : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 39.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2FLS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 8000 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.5 0.2 M SODIUM ACETATE, MICROBATCH, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.77800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.88900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.88900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.77800 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: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 348 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. 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 27 102.81 -167.73 REMARK 500 ILE A 41 43.75 -140.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 453 DISTANCE = 5.96 ANGSTROMS 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 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 44 O REMARK 620 2 LYS A 44 O 42.5 REMARK 620 3 HOH A 322 O 102.2 99.5 REMARK 620 4 HOH A 376 O 87.5 108.6 146.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 49 O REMARK 620 2 HOH A 342 O 115.1 REMARK 620 N 1 DBREF 7NCV A 1 107 UNP A8IYH1 A8IYH1_CHLRE 1 107 SEQRES 1 A 107 MET GLY LYS ALA GLU ALA ILE ASN GLU ILE GLN LYS ALA SEQRES 2 A 107 VAL ALA SER ASN LYS VAL ILE VAL TYR SER LYS THR TYR SEQRES 3 A 107 CYS PRO TYR CYS VAL LYS ALA LYS ASN ALA LEU ASN GLN SEQRES 4 A 107 PHE ILE ALA GLY LYS TYR THR VAL VAL GLU LEU GLU ASN SEQRES 5 A 107 ARG ALA ASP CSO ASP ALA MET GLN ASP ALA LEU LEU ASP SEQRES 6 A 107 ILE THR GLY GLY ARG SER VAL PRO ARG VAL PHE ILE ASN SEQRES 7 A 107 GLY LYS PHE LEU GLY GLY GLY ASP ASP THR ALA ALA ALA SEQRES 8 A 107 ALA SER ASN GLY THR LEU GLU LYS LEU LEU GLN GLU ALA SEQRES 9 A 107 GLY ALA LEU MODRES 7NCV CSO A 56 CYS MODIFIED RESIDUE HET CSO A 56 7 HET ACT A 201 4 HET NA A 202 1 HET NA A 203 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM ACT ACETATE ION HETNAM NA SODIUM ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *153(H2 O) HELIX 1 AA1 GLY A 2 ASN A 17 1 16 HELIX 2 AA2 CYS A 27 ALA A 42 1 16 HELIX 3 AA3 ASP A 55 GLY A 68 1 14 HELIX 4 AA4 GLY A 84 GLY A 95 1 12 HELIX 5 AA5 GLY A 95 ALA A 104 1 10 SHEET 1 AA1 4 THR A 46 GLU A 49 0 SHEET 2 AA1 4 VAL A 19 SER A 23 1 N SER A 23 O VAL A 48 SHEET 3 AA1 4 ARG A 74 ILE A 77 -1 O PHE A 76 N ILE A 20 SHEET 4 AA1 4 LYS A 80 GLY A 83 -1 O LEU A 82 N VAL A 75 LINK C ASP A 55 N CSO A 56 1555 1555 1.32 LINK C CSO A 56 N ASP A 57 1555 1555 1.34 LINK O ALYS A 44 NA NA A 202 1555 1555 3.06 LINK O BLYS A 44 NA NA A 202 1555 1555 2.47 LINK O GLU A 49 NA NA A 203 1555 1555 2.84 LINK NA NA A 202 O HOH A 322 1555 1555 2.80 LINK NA NA A 202 O HOH A 376 1555 1555 2.78 LINK NA NA A 203 O HOH A 342 1555 1555 2.74 CISPEP 1 VAL A 72 PRO A 73 0 -0.13 CRYST1 45.648 45.648 104.667 90.00 90.00 120.00 P 32 2 1 6 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 0.021907 0.012648 0.000000 0.00000 SCALE2 0.000000 0.025296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009554 0.00000