HEADER ELECTRON TRANSPORT 05-DEC-18 6Q46 TITLE CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN H1 FROM CHLAMYDOMONAS TITLE 2 REINHARDTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN H-TYPE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRX-H,THIOREDOXIN-CH1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 GENE: TRXH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALFA-BETA PROTEIN, THIOREDOXIN FOLD, DISULPHIDE OXIDOREDUCTASE, CELL KEYWDS 2 REDOX HOMEOSTATIS, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,M.ZAFFAGNINI,S.D.LEMAIRE REVDAT 2 24-JAN-24 6Q46 1 JRNL REVDAT 1 16-JAN-19 6Q46 0 JRNL AUTH C.H.MARCHAND,S.FERMANI,J.ROSSI,L.GURRIERI,D.TEDESCO,J.HENRI, JRNL AUTH 2 F.SPARLA,P.TROST,S.D.LEMAIRE,M.ZAFFAGNINI JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO THE REACTIVITY OF JRNL TITL 2 THIOREDOXIN H1 FROMCHLAMYDOMONAS REINHARDTII. JRNL REF ANTIOXIDANTS (BASEL) V. 8 2019 JRNL REFN ESSN 2076-3921 JRNL PMID 30609656 JRNL DOI 10.3390/ANTIOX8010010 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 22475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1083 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 42.2480 - 3.3995 0.99 2872 138 0.1568 0.1763 REMARK 3 2 3.3995 - 2.6984 1.00 2694 171 0.1959 0.2391 REMARK 3 3 2.6984 - 2.3574 0.99 2686 138 0.2063 0.2559 REMARK 3 4 2.3574 - 2.1418 0.99 2631 143 0.1997 0.2333 REMARK 3 5 2.1418 - 1.9883 0.99 2676 119 0.2075 0.2579 REMARK 3 6 1.9883 - 1.8711 0.99 2618 103 0.2083 0.2564 REMARK 3 7 1.8711 - 1.7774 0.98 2651 111 0.2444 0.2931 REMARK 3 8 1.7774 - 1.7000 0.98 2564 160 0.2633 0.2845 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 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 1712 REMARK 3 ANGLE : 0.743 2332 REMARK 3 CHIRALITY : 0.059 276 REMARK 3 PLANARITY : 0.005 295 REMARK 3 DIHEDRAL : 2.505 1198 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 6Q46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SILICON (1 1 1) CHANNEL-CUT REMARK 200 OPTICS : SILICON TOROIDAL MIRROR COATED REMARK 200 WITH RHODIUM REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22494 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.85800 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: 1EP7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8K, 10% (W/V) PEG 10K, REMARK 280 0.1 M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 47.97667 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 95.95333 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 95.95333 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 47.97667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 0 REMARK 465 MET B 0 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 ALA A 111 1.70 -68.58 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 289 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 290 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH B 302 DISTANCE = 5.91 ANGSTROMS DBREF 6Q46 A 0 112 UNP P80028 TRXH_CHLRE 1 113 DBREF 6Q46 B 0 112 UNP P80028 TRXH_CHLRE 1 113 SEQRES 1 A 113 MET GLY GLY SER VAL ILE VAL ILE ASP SER LYS ALA ALA SEQRES 2 A 113 TRP ASP ALA GLN LEU ALA LYS GLY LYS GLU GLU HIS LYS SEQRES 3 A 113 PRO ILE VAL VAL ASP PHE THR ALA THR TRP CYS GLY PRO SEQRES 4 A 113 CYS LYS MET ILE ALA PRO LEU PHE GLU THR LEU SER ASN SEQRES 5 A 113 ASP TYR ALA GLY LYS VAL ILE PHE LEU LYS VAL ASP VAL SEQRES 6 A 113 ASP ALA VAL ALA ALA VAL ALA GLU ALA ALA GLY ILE THR SEQRES 7 A 113 ALA MET PRO THR PHE HIS VAL TYR LYS ASP GLY VAL LYS SEQRES 8 A 113 ALA ASP ASP LEU VAL GLY ALA SER GLN ASP LYS LEU LYS SEQRES 9 A 113 ALA LEU VAL ALA LYS HIS ALA ALA ALA SEQRES 1 B 113 MET GLY GLY SER VAL ILE VAL ILE ASP SER LYS ALA ALA SEQRES 2 B 113 TRP ASP ALA GLN LEU ALA LYS GLY LYS GLU GLU HIS LYS SEQRES 3 B 113 PRO ILE VAL VAL ASP PHE THR ALA THR TRP CYS GLY PRO SEQRES 4 B 113 CYS LYS MET ILE ALA PRO LEU PHE GLU THR LEU SER ASN SEQRES 5 B 113 ASP TYR ALA GLY LYS VAL ILE PHE LEU LYS VAL ASP VAL SEQRES 6 B 113 ASP ALA VAL ALA ALA VAL ALA GLU ALA ALA GLY ILE THR SEQRES 7 B 113 ALA MET PRO THR PHE HIS VAL TYR LYS ASP GLY VAL LYS SEQRES 8 B 113 ALA ASP ASP LEU VAL GLY ALA SER GLN ASP LYS LEU LYS SEQRES 9 B 113 ALA LEU VAL ALA LYS HIS ALA ALA ALA FORMUL 3 HOH *192(H2 O) HELIX 1 AA1 SER A 9 HIS A 24 1 16 HELIX 2 AA2 CYS A 36 TYR A 53 1 18 HELIX 3 AA3 VAL A 67 ALA A 74 1 8 HELIX 4 AA4 SER A 98 ALA A 111 1 14 HELIX 5 AA5 SER B 9 HIS B 24 1 16 HELIX 6 AA6 CYS B 36 TYR B 53 1 18 HELIX 7 AA7 VAL B 67 ALA B 74 1 8 HELIX 8 AA8 SER B 98 ALA B 112 1 15 SHEET 1 AA1 5 ILE A 5 VAL A 6 0 SHEET 2 AA1 5 ILE A 58 ASP A 63 1 O PHE A 59 N ILE A 5 SHEET 3 AA1 5 ILE A 27 THR A 32 1 N VAL A 28 O ILE A 58 SHEET 4 AA1 5 THR A 81 LYS A 86 -1 O THR A 81 N PHE A 31 SHEET 5 AA1 5 VAL A 89 VAL A 95 -1 O ALA A 91 N VAL A 84 SHEET 1 AA2 5 ILE B 5 ILE B 7 0 SHEET 2 AA2 5 ILE B 58 ASP B 63 1 O PHE B 59 N ILE B 5 SHEET 3 AA2 5 ILE B 27 THR B 32 1 N VAL B 28 O ILE B 58 SHEET 4 AA2 5 THR B 81 LYS B 86 -1 O THR B 81 N PHE B 31 SHEET 5 AA2 5 VAL B 89 VAL B 95 -1 O ALA B 91 N VAL B 84 CISPEP 1 MET A 79 PRO A 80 0 -3.23 CISPEP 2 MET B 79 PRO B 80 0 -8.27 CRYST1 48.769 48.769 143.930 90.00 90.00 120.00 P 31 2 1 12 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 0.020505 0.011839 0.000000 0.00000 SCALE2 0.000000 0.023677 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006948 0.00000