HEADER OXIDOREDUCTASE 29-JAN-21 7NCW TITLE CRYSTAL STRUCTURE OF OXIDIZED 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 7NCW 1 JRNL REVDAT 2 16-JUN-21 7NCW 1 JRNL REVDAT 1 26-MAY-21 7NCW 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 5182 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 236 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 14.3000 - 3.0200 1.00 2530 130 0.1875 0.2257 REMARK 3 2 3.0200 - 2.4000 0.99 2416 106 0.2170 0.2384 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) : 0.197 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.53 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 : 0.002 805 REMARK 3 ANGLE : 0.421 1084 REMARK 3 CHIRALITY : 0.040 125 REMARK 3 PLANARITY : 0.002 143 REMARK 3 DIHEDRAL : 16.046 295 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): 3.5745 -19.7896 -9.9652 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.1602 REMARK 3 T33: 0.1167 T12: -0.0336 REMARK 3 T13: 0.0151 T23: -0.0517 REMARK 3 L TENSOR REMARK 3 L11: 2.6469 L22: 2.2112 REMARK 3 L33: 3.4375 L12: 1.0290 REMARK 3 L13: -0.1384 L23: 0.2806 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: -0.0098 S13: 0.0267 REMARK 3 S21: -0.0845 S22: -0.0865 S23: 0.1249 REMARK 3 S31: 0.0339 S32: -0.4519 S33: -0.0224 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 7NCW 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_1292113747. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION SUPERNOVA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.540562 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5212 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 14.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 (%): 54.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 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 69.49200 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 34.74600 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 34.74600 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 69.49200 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: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 360 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 96.72 -164.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7NCW 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 7NCW CSO A 56 CYS MODIFIED RESIDUE HET CSO A 56 7 HET ACT A 201 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM ACT ACETATE ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *92(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 SSBOND 1 CYS A 27 CYS A 30 1555 1555 2.04 LINK C ASP A 55 N CSO A 56 1555 1555 1.33 LINK C CSO A 56 N ASP A 57 1555 1555 1.33 CISPEP 1 VAL A 72 PRO A 73 0 1.01 CRYST1 45.383 45.383 104.238 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 0.022035 0.012722 0.000000 0.00000 SCALE2 0.000000 0.025443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009593 0.00000