HEADER OXIDOREDUCTASE 19-JUL-19 6KIL TITLE N21Q MUTANT THIOREDOXIN FROM HALOBACTERIUM SALINARUM NRC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRXA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM (STRAIN ATCC 700922 / SOURCE 3 JCM 11081 / NRC-1); SOURCE 4 ORGANISM_TAXID: 64091; SOURCE 5 STRAIN: ATCC 700922 / JCM 11081 / NRC-1; SOURCE 6 GENE: TRXA, TRXA1_1, TRXA1_2, VNG_6073G, VNG_6453G; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD-I KEYWDS OXIDOREDUCTASE, HALOPHILE EXPDTA X-RAY DIFFRACTION AUTHOR S.ARAI,C.SHIBAZAKI,R.SHIMIZU,M.ADACHI,M.ISHIBASHI,H.TOKUNAGA, AUTHOR 2 M.TOKUNAGA REVDAT 2 22-NOV-23 6KIL 1 REMARK REVDAT 1 15-JAN-20 6KIL 0 JRNL AUTH S.ARAI,C.SHIBAZAKI,R.SHIMIZU,M.ADACHI,M.ISHIBASHI, JRNL AUTH 2 H.TOKUNAGA,M.TOKUNAGA JRNL TITL CATALYTIC MECHANISM AND EVOLUTIONAL CHARACTERISTICS OF JRNL TITL 2 THIOREDOXIN FROM HALOBACTERIUM SALINARUM NRC-1. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 76 73 2020 JRNL REFN ESSN 1399-0047 JRNL DOI 10.1107/S2059798319015894 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 662 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 32.7100 - 2.7300 1.00 2628 139 0.1671 0.1701 REMARK 3 2 2.7300 - 2.1700 1.00 2523 135 0.1815 0.1792 REMARK 3 3 2.1700 - 1.9000 1.00 2509 129 0.1814 0.2001 REMARK 3 4 1.9000 - 1.7200 1.00 2471 133 0.1818 0.2090 REMARK 3 5 1.7200 - 1.6000 1.00 2482 126 0.1995 0.2414 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) : 0.075 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.06 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 : 0.005 908 REMARK 3 ANGLE : 1.051 1257 REMARK 3 CHIRALITY : 0.056 149 REMARK 3 PLANARITY : 0.008 174 REMARK 3 DIHEDRAL : 2.323 740 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 32.8646 26.4296 22.4906 REMARK 3 T TENSOR REMARK 3 T11: 0.0472 T22: 0.0677 REMARK 3 T33: 0.0601 T12: -0.0033 REMARK 3 T13: -0.0042 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 2.4894 L22: 2.4253 REMARK 3 L33: 2.6965 L12: -0.4263 REMARK 3 L13: -0.6234 L23: 0.2145 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: 0.0349 S13: -0.0768 REMARK 3 S21: 0.0494 S22: 0.0096 S23: 0.0037 REMARK 3 S31: 0.0537 S32: -0.0548 S33: -0.0086 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 6KIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 - 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : FIXED EXIT SI (111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13317 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38300 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: PHASER REMARK 200 STARTING MODEL: 2E0Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL BUFFER (PH8.5), 2.0 M REMARK 280 AMMONIUM SULFATE, 12.7 MG/ML OF PROTEIN, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 20.45850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.21750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.64150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.21750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.45850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.64150 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: 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 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 ARG A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 ASP A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 52 O HOH A 201 2.09 REMARK 500 OE1 GLN A 21 O HOH A 202 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 122 C - N - CA ANGL. DEV. = -13.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 74 50.72 -143.69 REMARK 500 VAL A 121 -116.80 -104.74 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 294 DISTANCE = 6.35 ANGSTROMS DBREF 6KIL A 2 119 UNP O46709 O46709_HALSA 2 119 SEQADV 6KIL ARG A -1 UNP O46709 EXPRESSION TAG SEQADV 6KIL GLY A 0 UNP O46709 EXPRESSION TAG SEQADV 6KIL SER A 1 UNP O46709 EXPRESSION TAG SEQADV 6KIL GLN A 21 UNP O46709 ASN 21 ENGINEERED MUTATION SEQADV 6KIL LEU A 120 UNP O46709 EXPRESSION TAG SEQADV 6KIL VAL A 121 UNP O46709 EXPRESSION TAG SEQADV 6KIL PRO A 122 UNP O46709 EXPRESSION TAG SEQRES 1 A 124 ARG GLY SER ALA THR ASP THR ALA ALA THR THR GLY THR SEQRES 2 A 124 ALA SER PRO ASP GLU PRO LEU TYR VAL GLN GLY GLN THR SEQRES 3 A 124 GLU LEU ASP ASP VAL THR SER ASP ASN ASP VAL VAL LEU SEQRES 4 A 124 ALA ASP PHE TYR ALA ASP TRP CYS GLY PRO CYS GLN MET SEQRES 5 A 124 LEU GLU PRO VAL VAL GLU THR LEU ALA GLU GLN THR ASP SEQRES 6 A 124 ALA ALA VAL ALA LYS ILE ASP VAL ASP GLU ASN GLN ALA SEQRES 7 A 124 LEU ALA SER ALA TYR GLY VAL ARG GLY VAL PRO THR LEU SEQRES 8 A 124 VAL LEU PHE ALA ASP GLY GLU GLN VAL GLU GLU VAL VAL SEQRES 9 A 124 GLY LEU GLN ASP GLU ASP ALA LEU LYS ASP LEU ILE GLU SEQRES 10 A 124 SER TYR THR GLU LEU VAL PRO FORMUL 2 HOH *94(H2 O) HELIX 1 AA1 GLY A 22 ASN A 33 1 12 HELIX 2 AA2 CYS A 45 THR A 62 1 18 HELIX 3 AA3 ASN A 74 TYR A 81 1 8 HELIX 4 AA4 ASP A 106 GLU A 119 1 14 SHEET 1 AA1 5 LEU A 18 TYR A 19 0 SHEET 2 AA1 5 ALA A 65 ASP A 70 1 O VAL A 66 N LEU A 18 SHEET 3 AA1 5 VAL A 35 TYR A 41 1 N ASP A 39 O ALA A 67 SHEET 4 AA1 5 THR A 88 ALA A 93 -1 O VAL A 90 N ALA A 38 SHEET 5 AA1 5 GLU A 96 VAL A 102 -1 O VAL A 101 N LEU A 89 CISPEP 1 VAL A 86 PRO A 87 0 -6.60 CRYST1 40.917 43.283 54.435 90.00 90.00 90.00 P 21 21 21 4 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 0.024440 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023104 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018371 0.00000