HEADER HYDROLASE 14-NOV-14 4WXT TITLE X-RAY CRYSTAL STRUCTURE OF THIOREDOXIN FROM MYCOBACTERIUM AVIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM AVIUM SUBSP. HOMINISSUIS 3388; SOURCE 3 ORGANISM_TAXID: 1160712; SOURCE 4 GENE: MAV3388_24025; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INFECTIOUS DISEASE, SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL KEYWDS 2 GENOMICS CENTER FOR INFECTIOUS DISEASE, THIOREDOXIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 27-SEP-23 4WXT 1 SOURCE REMARK REVDAT 1 26-NOV-14 4WXT 0 JRNL AUTH C.M.LUKACS,T.ARAKAKI,D.D.DON LORIMER,T.E.EDWARDS JRNL TITL X-RAY CRYSTAL STRUCTURE OF THIOREDOXIN FROM MYCOBACTERIUM JRNL TITL 2 AVIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1839) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 25236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1232 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 30.8322 - 2.4960 0.98 2772 132 0.1413 0.1601 REMARK 3 2 2.4960 - 1.9813 0.97 2744 139 0.1509 0.1959 REMARK 3 3 1.9813 - 1.7308 0.96 2723 118 0.1596 0.1737 REMARK 3 4 1.7308 - 1.5726 0.95 2705 136 0.1615 0.1651 REMARK 3 5 1.5726 - 1.4599 0.94 2691 124 0.1647 0.1647 REMARK 3 6 1.4599 - 1.3738 0.94 2604 166 0.1807 0.1883 REMARK 3 7 1.3738 - 1.3050 0.93 2596 135 0.1833 0.1891 REMARK 3 8 1.3050 - 1.2482 0.92 2578 158 0.1877 0.1974 REMARK 3 9 1.2482 - 1.2001 0.91 2591 124 0.2010 0.2254 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 850 REMARK 3 ANGLE : 1.352 1168 REMARK 3 CHIRALITY : 0.065 141 REMARK 3 PLANARITY : 0.008 153 REMARK 3 DIHEDRAL : 11.153 310 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 8 THROUGH 115) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1421 -0.3480 -1.5849 REMARK 3 T TENSOR REMARK 3 T11: 0.0615 T22: 0.0445 REMARK 3 T33: 0.0586 T12: 0.0000 REMARK 3 T13: -0.0052 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 1.6324 L22: 0.3719 REMARK 3 L33: 1.0555 L12: -0.0611 REMARK 3 L13: -0.3527 L23: -0.1018 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: 0.0391 S13: -0.0276 REMARK 3 S21: -0.0437 S22: 0.0101 S23: 0.0437 REMARK 3 S31: -0.0217 S32: -0.0188 S33: 0.0345 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 4WXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25241 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 5.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2I1U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: JCSG+ B2: 20% PEG 3350 0.2 M SODIUM REMARK 280 THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 MET A -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 ALA A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 ALA A 7 REMARK 465 LEU A 116 REMARK 465 GLY A 117 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 GLN A 74 CG CD OE1 NE2 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 OE1 GLU A 54 O HOH A 201 2.08 REMARK 500 O HOH A 265 O HOH A 277 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 276 O HOH A 284 1565 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SSGCID-MYAVA.00058.A RELATED DB: TARGETTRACK DBREF1 4WXT A 1 117 UNP A0A067HWN0_MYCAV DBREF2 4WXT A A0A067HWN0 1 117 SEQADV 4WXT MET A -7 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT ALA A -6 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A -5 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A -4 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A -3 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A -2 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A -1 UNP A0A067HWN EXPRESSION TAG SEQADV 4WXT HIS A 0 UNP A0A067HWN EXPRESSION TAG SEQRES 1 A 125 MET ALA HIS HIS HIS HIS HIS HIS MET THR ASP ALA GLU SEQRES 2 A 125 LYS ALA ILE ALA THR ILE GLU VAL SER ASP ALA SER PHE SEQRES 3 A 125 SER THR ASP VAL LEU ALA SER ASN LYS PRO VAL LEU VAL SEQRES 4 A 125 ASP PHE TRP ALA THR TRP CYS GLY PRO CYS LYS MET VAL SEQRES 5 A 125 ALA PRO VAL LEU GLU GLU ILE ALA SER GLU ARG GLY ASP SEQRES 6 A 125 HIS LEU THR VAL ALA LYS LEU ASP VAL ASP ALA ASN PRO SEQRES 7 A 125 GLU THR ALA GLN ASN PHE GLN VAL VAL SER ILE PRO THR SEQRES 8 A 125 LEU ILE LEU PHE LYS ASP GLY GLN PRO VAL LYS ARG ILE SEQRES 9 A 125 VAL GLY ALA LYS GLY LYS ALA ALA LEU LEU ARG GLU LEU SEQRES 10 A 125 SER ASP ALA VAL PRO ASN LEU GLY FORMUL 2 HOH *139(H2 O) HELIX 1 AA1 SER A 17 VAL A 22 1 6 HELIX 2 AA2 CYS A 38 ARG A 55 1 18 HELIX 3 AA3 ASN A 69 PHE A 76 1 8 HELIX 4 AA4 GLY A 101 SER A 110 1 10 SHEET 1 AA1 5 ILE A 11 GLU A 12 0 SHEET 2 AA1 5 THR A 60 ASP A 65 1 O LYS A 63 N ILE A 11 SHEET 3 AA1 5 VAL A 29 TRP A 34 1 N ASP A 32 O ALA A 62 SHEET 4 AA1 5 THR A 83 LYS A 88 -1 O THR A 83 N PHE A 33 SHEET 5 AA1 5 GLN A 91 VAL A 97 -1 O VAL A 93 N LEU A 86 SSBOND 1 CYS A 38 CYS A 41 1555 1555 2.17 CISPEP 1 ILE A 81 PRO A 82 0 -0.50 CRYST1 26.070 29.860 31.080 82.64 87.64 66.84 P 1 1 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 0.038358 -0.016410 0.000427 0.00000 SCALE2 0.000000 0.036426 -0.004475 0.00000 SCALE3 0.000000 0.000000 0.032444 0.00000