HEADER OXIDOREDUCTASE 18-APR-16 5G31 TITLE CRYSTALLOGRAPHIC STRUCTURE OF MUTANT C73S OF THIOREDOXIN FROM TITLE 2 LITOPENAEUS VANNAMEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.8.1.9; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN COMPND 8 THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LITOPENAEUS VANNAMEI; SOURCE 3 ORGANISM_COMMON: PACIFIC WHITE SHRIMP; SOURCE 4 ORGANISM_TAXID: 6689; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS OXIDOREDUCTASE, THIOREDOXIN, SHRIMP, LITOPENAEUS VANNAMEI, MUTANT, KEYWDS 2 DISULFIDE BOND EXPDTA X-RAY DIFFRACTION AUTHOR A.A.CAMPOS-ACEVEDO,E.RUDINO-PINERA REVDAT 4 10-JAN-24 5G31 1 REMARK LINK REVDAT 3 19-APR-17 5G31 1 JRNL REVDAT 2 12-APR-17 5G31 1 JRNL REVDAT 1 15-MAR-17 5G31 0 JRNL AUTH A.A.CAMPOS-ACEVEDO,R.R.SOTELO-MUNDO,J.PEREZ,E.RUDINO-PINERA JRNL TITL IS DIMERIZATION A COMMON FEATURE IN THIOREDOXINS? THE CASE JRNL TITL 2 OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 326 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28375144 JRNL DOI 10.1107/S2059798317002066 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8198 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 820 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 44.8730 - 3.6337 1.00 1321 147 0.1984 0.1967 REMARK 3 2 3.6337 - 2.8843 1.00 1238 138 0.2085 0.2627 REMARK 3 3 2.8843 - 2.5198 1.00 1221 135 0.2200 0.2717 REMARK 3 4 2.5198 - 2.2894 1.00 1205 134 0.2160 0.2868 REMARK 3 5 2.2894 - 2.1253 1.00 1194 133 0.2176 0.2631 REMARK 3 6 2.1253 - 2.0000 1.00 1199 133 0.2178 0.2764 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.66 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 : 0.008 892 REMARK 3 ANGLE : 0.908 1210 REMARK 3 CHIRALITY : 0.054 133 REMARK 3 PLANARITY : 0.005 162 REMARK 3 DIHEDRAL : 13.034 560 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 5G31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-16. REMARK 100 THE DEPOSITION ID IS D_1290066692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 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: PDB ENTRY 3ZZX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % (W/V) POLYETHYLENE GLYCOL 3,000. REMARK 280 100 MM IMIDAZOLE PH 8.0. 200 MM ZINC ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.72200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.14850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.72200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.72200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.14850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.72200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.72200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.14850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.72200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.72200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.14850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2025 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2046 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2054 LIES ON A SPECIAL POSITION. 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 OD2 ASP A 51 O HOH A 2031 1.86 REMARK 500 O HOH A 2031 O HOH A 2032 1.94 REMARK 500 NZ LYS A 105 O HOH A 2031 2.02 REMARK 500 O HOH A 2011 O HOH A 2038 2.05 REMARK 500 OD2 ASP A 60 O HOH A 2023 2.07 REMARK 500 OD2 ASP A 95 O HOH A 2045 2.09 REMARK 500 O HOH A 2022 O HOH A 2023 2.14 REMARK 500 OE1 GLU A 44 O HOH A 2027 2.15 REMARK 500 N MET A 1 OE1 GLN A 47 2.17 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 ALA A 92 49.23 -101.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 60 O REMARK 620 2 GLU A 63 OE2 86.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G2Z RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF MUTANT W31A OF THIOREDOXIN FROM REMARK 900 LITOPENAEUS VANNAMEI REMARK 900 RELATED ID: 5G30 RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF MUTANT D60S OF THIOREDOXIN FROM REMARK 900 LITOPENAEUS VANNAMEI REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT REMARK 999 B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENILALANINE DBREF 5G31 A 1 105 UNP B1PWB9 B1PWB9_LITVA 1 105 SEQADV 5G31 PHE A 11 UNP B1PWB9 SER 11 CONFLICT SEQADV 5G31 SER A 73 UNP B1PWB9 CYS 73 ENGINEERED MUTATION SEQRES 1 A 105 MET VAL TYR GLN VAL LYS ASP GLN GLU ASP PHE THR LYS SEQRES 2 A 105 GLN LEU ASN GLU ALA GLY ASN LYS LEU VAL VAL ILE ASP SEQRES 3 A 105 PHE TYR ALA THR TRP CYS GLY PRO CYS LYS MET ILE ALA SEQRES 4 A 105 PRO LYS LEU GLU GLU LEU SER GLN SER MET SER ASP VAL SEQRES 5 A 105 VAL PHE LEU LYS VAL ASP VAL ASP GLU CYS GLU ASP ILE SEQRES 6 A 105 ALA GLN ASP ASN GLN ILE ALA SER MET PRO THR PHE LEU SEQRES 7 A 105 PHE MET LYS ASN GLY GLN LYS LEU ASP SER LEU SER GLY SEQRES 8 A 105 ALA ASN TYR ASP LYS LEU LEU GLU LEU VAL GLU LYS ASN SEQRES 9 A 105 LYS HET ZN A1106 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *54(H2 O) HELIX 1 1 ASP A 7 ALA A 18 1 12 HELIX 2 2 CYS A 32 MET A 49 1 18 HELIX 3 3 CYS A 62 ASN A 69 1 8 HELIX 4 4 ASN A 93 LYS A 105 1 13 SHEET 1 AA 5 TYR A 3 GLN A 4 0 SHEET 2 AA 5 VAL A 52 ASP A 58 1 O PHE A 54 N TYR A 3 SHEET 3 AA 5 LEU A 22 TYR A 28 1 O LEU A 22 N VAL A 53 SHEET 4 AA 5 THR A 76 LYS A 81 -1 O THR A 76 N PHE A 27 SHEET 5 AA 5 GLN A 84 SER A 90 -1 O GLN A 84 N LYS A 81 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.07 LINK O ASP A 60 ZN ZN A1106 1555 1555 2.03 LINK OE2 GLU A 63 ZN ZN A1106 1555 1555 2.10 CISPEP 1 MET A 74 PRO A 75 0 -1.28 CISPEP 2 MET A 74 PRO A 75 0 -3.80 SITE 1 AC1 2 ASP A 60 GLU A 63 CRYST1 63.444 63.444 56.297 90.00 90.00 90.00 P 42 21 2 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 0.015762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017763 0.00000