HEADER OXIDOREDUCTASE 10-OCT-14 4V2N TITLE CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: TITLE 2 RADIATION DAMAGE EFFECT AT 85 MGY, FOCUSED IN DISULFIDE BONDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A, B; 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_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS OXIDOREDUCTASE, LITOPENAEUS VANNAMEI, DISULFIDE BOND EXPDTA X-RAY DIFFRACTION AUTHOR A.A.CAMPOS-ACEVEDO,E.RUDINO-PINERA REVDAT 2 10-JAN-24 4V2N 1 REMARK REVDAT 1 14-JAN-15 4V2N 0 JRNL AUTH A.A.CAMPOS-ACEVEDO,E.RUDINO-PINERA JRNL TITL CRYSTALLOGRAPHIC STUDIES EVIDENCING THE HIGH ENERGY JRNL TITL 2 TOLERANCE TO DISRUPTING THE INTERFACE DISULFIDE BOND OF JRNL TITL 3 THIOREDOXIN 1 FROM WHITE LEG SHRIMP LITOPENAEUS VANNAMEI. JRNL REF MOLECULES V. 19 21113 2014 JRNL REFN ESSN 1420-3049 JRNL PMID 25517346 JRNL DOI 10.3390/MOLECULES191221113 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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 28.8541 - 3.4121 0.99 3033 145 0.1666 0.2363 REMARK 3 2 3.4121 - 2.7089 1.00 2951 162 0.1920 0.2310 REMARK 3 3 2.7089 - 2.3667 1.00 2952 149 0.1904 0.2556 REMARK 3 4 2.3667 - 2.1504 1.00 2911 145 0.1973 0.3125 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.45 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 1844 REMARK 3 ANGLE : 1.055 2496 REMARK 3 CHIRALITY : 0.039 275 REMARK 3 PLANARITY : 0.005 328 REMARK 3 DIHEDRAL : 13.785 724 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 4V2N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1290061959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12470 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 28.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULPHATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,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 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 78.68600 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 39.34300 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 39.34300 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 78.68600 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 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: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.3 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 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 2035 O HOH B 2024 4667 2.18 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 CYS A 62 63.68 -117.48 REMARK 500 ALA A 72 -30.79 -136.37 REMARK 500 ALA A 92 49.66 -95.35 REMARK 500 CYS B 62 62.15 -117.87 REMARK 500 ALA B 72 -84.39 -133.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V2L RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: REMARK 900 RADIATION DAMAGE EFFECT AT 3.4 MGY, FOCUSED IN DISULFIDE BONDS. REMARK 900 RELATED ID: 4V2M RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI: REMARK 900 RADIATION DAMAGE EFFECT AT 34 MGY, FOCUSED IN DISULFIDE BONDS. 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 PHENYLALANINE DBREF 4V2N A 1 105 UNP B1PWB9 B1PWB9_LITVA 1 105 DBREF 4V2N B 1 105 UNP B1PWB9 B1PWB9_LITVA 1 105 SEQADV 4V2N PHE A 11 UNP B1PWB9 SER 11 ENGINEERED MUTATION SEQADV 4V2N PHE B 11 UNP B1PWB9 SER 11 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 CYS 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 SEQRES 1 B 105 MET VAL TYR GLN VAL LYS ASP GLN GLU ASP PHE THR LYS SEQRES 2 B 105 GLN LEU ASN GLU ALA GLY ASN LYS LEU VAL VAL ILE ASP SEQRES 3 B 105 PHE TYR ALA THR TRP CYS GLY PRO CYS LYS MET ILE ALA SEQRES 4 B 105 PRO LYS LEU GLU GLU LEU SER GLN SER MET SER ASP VAL SEQRES 5 B 105 VAL PHE LEU LYS VAL ASP VAL ASP GLU CYS GLU ASP ILE SEQRES 6 B 105 ALA GLN ASP ASN GLN ILE ALA CYS MET PRO THR PHE LEU SEQRES 7 B 105 PHE MET LYS ASN GLY GLN LYS LEU ASP SER LEU SER GLY SEQRES 8 B 105 ALA ASN TYR ASP LYS LEU LEU GLU LEU VAL GLU LYS ASN SEQRES 9 B 105 LYS HET ACT A1106 4 HET SO4 B1106 5 HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *68(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 HELIX 5 5 ASP B 7 ALA B 18 1 12 HELIX 6 6 CYS B 32 MET B 49 1 18 HELIX 7 7 CYS B 62 ASN B 69 1 8 HELIX 8 8 ASN B 93 LYS B 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 SHEET 1 BA 5 TYR B 3 GLN B 4 0 SHEET 2 BA 5 VAL B 52 ASP B 58 1 O PHE B 54 N TYR B 3 SHEET 3 BA 5 LEU B 22 TYR B 28 1 O LEU B 22 N VAL B 53 SHEET 4 BA 5 THR B 76 LYS B 81 -1 O THR B 76 N PHE B 27 SHEET 5 BA 5 GLN B 84 SER B 90 -1 O GLN B 84 N LYS B 81 CISPEP 1 MET A 74 PRO A 75 0 -6.32 CISPEP 2 MET B 74 PRO B 75 0 -0.35 CISPEP 3 MET B 74 PRO B 75 0 0.66 SITE 1 AC1 6 LEU A 15 ASN A 16 GLY A 19 ASN A 82 SITE 2 AC1 6 GLY A 83 LYS B 41 SITE 1 AC2 5 LYS B 13 GLU B 17 ALA B 18 ASN B 20 SITE 2 AC2 5 LYS B 21 CRYST1 57.703 57.703 118.029 90.00 90.00 120.00 P 32 1 2 12 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 0.017330 0.010006 0.000000 0.00000 SCALE2 0.000000 0.020011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008472 0.00000