HEADER OXIDOREDUCTASE 07-MAY-09 3HDC TITLE THE CRYSTAL STRUCTURE OF THIOREDOXIN PROTEIN FROM GEOBACTER TITLE 2 METALLIREDUCENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS GS-15; SOURCE 3 ORGANISM_TAXID: 269799; SOURCE 4 STRAIN: STRAIN GS-15 / ATCC 53774 / DSM 7210; SOURCE 5 GENE: GMET_1383; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODON+RIL-STRATAGENE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3(BC) KEYWDS THIOREDOXIN, GEOBACTER METALLIREDUCENS, GS-15, ATCC53774, DSM 7210, KEYWDS 2 11211I, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, KEYWDS 4 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 3 10-FEB-21 3HDC 1 AUTHOR JRNL REVDAT 2 13-NOV-19 3HDC 1 KEYWDS LINK REVDAT 1 26-MAY-09 3HDC 0 JRNL AUTH Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN JRNL TITL THE CRYSTAL STRUCTURE OF THIOREDOXIN PROTEIN FROM GEOBACTER JRNL TITL 2 METALLIREDUCENS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 21827 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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 35.9073 - 3.5417 0.99 2740 159 0.1810 0.1747 REMARK 3 2 3.5417 - 2.8115 1.00 2669 135 0.1831 0.1897 REMARK 3 3 2.8115 - 2.4562 0.99 2632 123 0.1947 0.2397 REMARK 3 4 2.4562 - 2.2317 0.99 2565 164 0.1757 0.1894 REMARK 3 5 2.2317 - 2.0717 0.99 2563 133 0.1649 0.2058 REMARK 3 6 2.0717 - 1.9496 0.98 2572 137 0.1609 0.2071 REMARK 3 7 1.9496 - 1.8520 0.97 2500 137 0.1591 0.2029 REMARK 3 8 1.8520 - 1.7714 0.96 2452 146 0.1645 0.1966 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 : 0.39 REMARK 3 B_SOL : 53.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.88180 REMARK 3 B22 (A**2) : 2.88180 REMARK 3 B33 (A**2) : -5.76360 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 3HDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21827 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 3.0 M SODIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, SITTING DROP 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 31.52900 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 63.05800 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 63.05800 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 31.52900 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 300 REMARK: DIMER, THE SECOND MOLECULE IS GENERATED BY THE TWO FOLD REMARK 300 AXIS: X-Y, -Y, Z+2/3. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.05800 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 MSE A 19 REMARK 465 GLY A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 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 SER A 114 55.77 -92.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11211I RELATED DB: TARGETDB DBREF 3HDC A 22 168 UNP Q39VV7 Q39VV7_GEOMG 22 168 SEQADV 3HDC MSE A 19 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC SER A 20 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC LEU A 21 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC GLU A 169 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC GLY A 170 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 171 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 172 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 173 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 174 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 175 UNP Q39VV7 EXPRESSION TAG SEQADV 3HDC HIS A 176 UNP Q39VV7 EXPRESSION TAG SEQRES 1 A 158 MSE SER LEU ALA PRO GLY LYS ALA GLU SER ASP ALA PRO SEQRES 2 A 158 LEU VAL ARG THR GLY ALA LEU ALA PRO ASN PHE LYS LEU SEQRES 3 A 158 PRO THR LEU SER GLY GLU ASN LYS SER LEU ALA GLN TYR SEQRES 4 A 158 ARG GLY LYS ILE VAL LEU VAL ASN PHE TRP ALA SER TRP SEQRES 5 A 158 CYS PRO TYR CYS ARG ASP GLU MSE PRO SER MSE ASP ARG SEQRES 6 A 158 LEU VAL LYS SER PHE PRO LYS GLY ASP LEU VAL VAL LEU SEQRES 7 A 158 ALA VAL ASN VAL GLU LYS ARG PHE PRO GLU LYS TYR ARG SEQRES 8 A 158 ARG ALA PRO VAL SER PHE ASN PHE LEU SER ASP ALA THR SEQRES 9 A 158 GLY GLN VAL GLN GLN ARG TYR GLY ALA ASN ARG LEU PRO SEQRES 10 A 158 ASP THR PHE ILE VAL ASP ARG LYS GLY ILE ILE ARG GLN SEQRES 11 A 158 ARG VAL THR GLY GLY ILE GLU TRP ASP ALA PRO LYS VAL SEQRES 12 A 158 VAL SER TYR LEU LYS SER LEU GLU GLY HIS HIS HIS HIS SEQRES 13 A 158 HIS HIS MODRES 3HDC MSE A 78 MET SELENOMETHIONINE MODRES 3HDC MSE A 81 MET SELENOMETHIONINE HET MSE A 78 8 HET MSE A 81 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *168(H2 O) HELIX 1 1 ALA A 55 ARG A 58 5 4 HELIX 2 2 CYS A 71 PHE A 88 1 18 HELIX 3 3 PRO A 105 ALA A 111 5 7 HELIX 4 4 GLY A 123 TYR A 129 1 7 HELIX 5 5 ALA A 158 SER A 167 1 10 SHEET 1 A 2 LYS A 43 PRO A 45 0 SHEET 2 A 2 ASN A 51 SER A 53 -1 O LYS A 52 N LEU A 44 SHEET 1 B 5 ASN A 116 SER A 119 0 SHEET 2 B 5 LEU A 93 ASN A 99 1 N ASN A 99 O LEU A 118 SHEET 3 B 5 ILE A 61 TRP A 67 1 N LEU A 63 O VAL A 94 SHEET 4 B 5 ASP A 136 VAL A 140 -1 O VAL A 140 N VAL A 62 SHEET 5 B 5 ILE A 146 THR A 151 -1 O VAL A 150 N THR A 137 LINK C GLU A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N PRO A 79 1555 1555 1.34 LINK C SER A 80 N MSE A 81 1555 1555 1.34 LINK C MSE A 81 N ASP A 82 1555 1555 1.33 CISPEP 1 LEU A 134 PRO A 135 0 -5.91 CRYST1 63.678 63.678 94.587 90.00 90.00 120.00 P 31 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 0.015704 0.009067 0.000000 0.00000 SCALE2 0.000000 0.018133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010572 0.00000