HEADER OXIDOREDUCTASE 18-MAR-22 7XAO TITLE CRYSTAL STRUCTURE OF THIOREDOXIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: TRXA, TRX; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRX1, THIOREDOXIN1, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.CHANG,H.H.PARK REVDAT 2 29-NOV-23 7XAO 1 REMARK REVDAT 1 01-JUN-22 7XAO 0 JRNL AUTH Y.J.CHANG,H.H.PARK JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII JRNL TITL 2 THIOREDOXIN 1. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 608 1 2022 JRNL REFN ESSN 1090-2104 JRNL PMID 35378360 JRNL DOI 10.1016/J.BBRC.2022.03.134 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 38802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 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 28.6800 - 3.4900 1.00 2850 155 0.2236 0.2690 REMARK 3 2 3.4900 - 2.7700 1.00 2730 149 0.2431 0.2667 REMARK 3 3 2.7700 - 2.4200 1.00 2646 142 0.2598 0.3141 REMARK 3 4 2.4200 - 2.2000 1.00 2659 141 0.2504 0.2867 REMARK 3 5 2.2000 - 2.0400 1.00 2642 147 0.2464 0.2544 REMARK 3 6 2.0400 - 1.9200 1.00 2614 141 0.2484 0.2852 REMARK 3 7 1.9200 - 1.8300 1.00 2582 141 0.2494 0.2753 REMARK 3 8 1.8300 - 1.7500 1.00 2595 144 0.2468 0.2992 REMARK 3 9 1.7500 - 1.6800 1.00 2627 139 0.2587 0.3266 REMARK 3 10 1.6800 - 1.6200 1.00 2586 139 0.2554 0.2925 REMARK 3 11 1.6200 - 1.5700 1.00 2549 139 0.2606 0.2979 REMARK 3 12 1.5700 - 1.5300 1.00 2610 145 0.2597 0.3054 REMARK 3 13 1.5300 - 1.4900 0.99 2496 131 0.2655 0.3144 REMARK 3 14 1.4900 - 1.4500 0.99 2622 141 0.2784 0.3131 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) : 0.203 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.78 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 1634 REMARK 3 ANGLE : 0.837 2234 REMARK 3 CHIRALITY : 0.083 274 REMARK 3 PLANARITY : 0.006 286 REMARK 3 DIHEDRAL : 4.947 216 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 7XAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 125 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 28.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.09338 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42130 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2YN1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SPG BUFFER/NAOH PH 5.7, 23% PEG REMARK 280 1500, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 15.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 107.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.63500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 CYS A 33 SG REMARK 470 CYS B 33 SG 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 VAL B 17 -59.15 -127.36 REMARK 500 ARG B 74 -53.68 76.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XAO A 2 108 UNP V5VGM8 V5VGM8_ACIBA 2 108 DBREF 7XAO B 2 108 UNP V5VGM8 V5VGM8_ACIBA 2 108 SEQRES 1 A 107 SER ALA THR ILE VAL ASN THR THR ASP ASP ASN PHE GLN SEQRES 2 A 107 ALA ASP VAL LEU ASP ALA GLU THR PRO VAL LEU VAL ASP SEQRES 3 A 107 PHE TRP ALA GLY TRP CYS ALA PRO CYS LYS ALA ILE ALA SEQRES 4 A 107 PRO VAL LEU GLU ASP LEU SER SER GLU TYR ALA GLY LYS SEQRES 5 A 107 VAL LYS ILE VAL LYS VAL ASP VAL THR SER CYS GLU GLU SEQRES 6 A 107 THR ALA VAL LYS TYR ASN ILE ARG ASN ILE PRO ALA LEU SEQRES 7 A 107 LEU LEU PHE LYS ASN GLY GLU VAL VAL ALA GLN GLN ILE SEQRES 8 A 107 GLY ALA VAL PRO ARG SER LYS LEU VAL SER PHE ILE ASP SEQRES 9 A 107 GLU ASN VAL SEQRES 1 B 107 SER ALA THR ILE VAL ASN THR THR ASP ASP ASN PHE GLN SEQRES 2 B 107 ALA ASP VAL LEU ASP ALA GLU THR PRO VAL LEU VAL ASP SEQRES 3 B 107 PHE TRP ALA GLY TRP CYS ALA PRO CYS LYS ALA ILE ALA SEQRES 4 B 107 PRO VAL LEU GLU ASP LEU SER SER GLU TYR ALA GLY LYS SEQRES 5 B 107 VAL LYS ILE VAL LYS VAL ASP VAL THR SER CYS GLU GLU SEQRES 6 B 107 THR ALA VAL LYS TYR ASN ILE ARG ASN ILE PRO ALA LEU SEQRES 7 B 107 LEU LEU PHE LYS ASN GLY GLU VAL VAL ALA GLN GLN ILE SEQRES 8 B 107 GLY ALA VAL PRO ARG SER LYS LEU VAL SER PHE ILE ASP SEQRES 9 B 107 GLU ASN VAL FORMUL 3 HOH *201(H2 O) HELIX 1 AA1 ASN A 12 VAL A 17 1 6 HELIX 2 AA2 CYS A 33 ILE A 39 1 7 HELIX 3 AA3 ILE A 39 TYR A 50 1 12 HELIX 4 AA4 CYS A 64 TYR A 71 1 8 HELIX 5 AA5 PRO A 96 ASN A 107 1 12 HELIX 6 AA6 ASN B 12 VAL B 17 1 6 HELIX 7 AA7 CYS B 33 TYR B 50 1 18 HELIX 8 AA8 CYS B 64 TYR B 71 1 8 HELIX 9 AA9 PRO B 96 VAL B 108 1 13 SHEET 1 AA1 5 VAL A 6 ASN A 7 0 SHEET 2 AA1 5 LYS A 55 ASP A 60 1 O LYS A 58 N VAL A 6 SHEET 3 AA1 5 VAL A 24 TRP A 29 1 N ASP A 27 O VAL A 57 SHEET 4 AA1 5 ALA A 78 LYS A 83 -1 O PHE A 82 N VAL A 24 SHEET 5 AA1 5 GLU A 86 ILE A 92 -1 O VAL A 88 N LEU A 81 SHEET 1 AA2 5 VAL B 6 ASN B 7 0 SHEET 2 AA2 5 LYS B 55 ASP B 60 1 O LYS B 58 N VAL B 6 SHEET 3 AA2 5 VAL B 24 TRP B 29 1 N LEU B 25 O LYS B 55 SHEET 4 AA2 5 ALA B 78 LYS B 83 -1 O PHE B 82 N VAL B 24 SHEET 5 AA2 5 GLU B 86 ILE B 92 -1 O GLN B 91 N LEU B 79 CISPEP 1 ILE A 76 PRO A 77 0 -0.58 CISPEP 2 ILE B 76 PRO B 77 0 -3.97 CRYST1 31.240 31.270 215.780 90.00 90.00 90.00 P 21 21 21 8 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 0.032010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031980 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004634 0.00000