HEADER OXIDOREDUCTASE 21-AUG-15 5DBQ TITLE CRYSTAL STRUCTURE OF INSECT THIOREDOXIN AT 1.95 ANGSTROMS 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: ANTICARSIA GEMMATALIS; SOURCE 3 ORGANISM_COMMON: VELVETBEAN CATERPILLAR; SOURCE 4 ORGANISM_TAXID: 129554; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 CODON PLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 28A(+) KEYWDS THIOREDOXIN, DISULFIDE BRIDGE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KLINKE,M.D.TEJEDOR,M.L.CERUTTI,R.GIACOMETTI,L.H.OTERO,F.A.GOLDBAUM, AUTHOR 2 J.A.ZAVALA,R.A.WOLOSIUK,E.A.PAGANO REVDAT 3 27-SEP-23 5DBQ 1 REMARK REVDAT 2 27-SEP-17 5DBQ 1 REMARK REVDAT 1 24-AUG-16 5DBQ 0 JRNL AUTH S.KLINKE,M.D.TEJEDOR,M.L.CERUTTI,R.GIACOMETTI,L.H.OTERO, JRNL AUTH 2 F.A.GOLDBAUM,J.A.ZAVALA,R.A.WOLOSIUK,E.A.PAGANO JRNL TITL CRYSTAL STRUCTURE OF INSECT THIOREDOXIN AT 1.95 ANGSTROMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 14272 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 714 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.37 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2834 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2563 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2692 REMARK 3 BIN R VALUE (WORKING SET) : 0.2557 REMARK 3 BIN FREE R VALUE : 0.2679 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.56970 REMARK 3 B22 (A**2) : -1.91050 REMARK 3 B33 (A**2) : -2.65920 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.07240 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.283 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.233 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.182 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.211 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.175 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1670 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2246 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 618 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 52 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 228 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1670 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 228 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2046 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.12 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.76 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.31 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : HELIOS MX MULTILAYER OPTICS REMARK 200 OPTICS : DIFFRACTOMETER: BRUKER D8 QUEST, REMARK 200 SOURCE: IMUS COPPER MICROFOCUS, REMARK 200 DETECTOR: PHOTON 100 REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON 100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.73500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP, MOLREP, PHASER REMARK 200 STARTING MODEL: PDB 1XWB REMARK 200 REMARK 200 REMARK: SMALL PRISMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 4000, 0.2 M SODIUM ACETATE, REMARK 280 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 53.85500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.85500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.49000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 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 B 291 DISTANCE = 6.60 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 CLONING ARTIFACT GSH AT THE N-TERMINUS AFTER THROMBIN CLEAVAGE. DBREF 5DBQ A -2 106 PDB 5DBQ 5DBQ -2 106 DBREF 5DBQ B -2 106 PDB 5DBQ 5DBQ -2 106 SEQRES 1 A 109 GLY SER HIS MET SER ILE HIS ILE LYS ASP SER ASP ASP SEQRES 2 A 109 LEU LYS THR ARG LEU ALA GLU ALA GLY ASP LYS LEU VAL SEQRES 3 A 109 VAL ILE ASP PHE MET ALA THR TRP CYS GLY PRO CYS LYS SEQRES 4 A 109 MET ILE GLY PRO LYS LEU ASP GLU MET ALA GLY GLU MET SEQRES 5 A 109 GLN ASP SER ILE VAL VAL VAL LYS VAL ASP VAL ASP GLU SEQRES 6 A 109 CYS GLU ASP ILE ALA THR GLU TYR ASN ILE ASN SER MET SEQRES 7 A 109 PRO THR PHE VAL PHE VAL LYS ASN GLY LYS LYS ILE GLU SEQRES 8 A 109 GLU PHE SER GLY ALA ASN VAL ASP LYS LEU ARG ASN THR SEQRES 9 A 109 ILE LEU LYS LEU LYS SEQRES 1 B 109 GLY SER HIS MET SER ILE HIS ILE LYS ASP SER ASP ASP SEQRES 2 B 109 LEU LYS THR ARG LEU ALA GLU ALA GLY ASP LYS LEU VAL SEQRES 3 B 109 VAL ILE ASP PHE MET ALA THR TRP CYS GLY PRO CYS LYS SEQRES 4 B 109 MET ILE GLY PRO LYS LEU ASP GLU MET ALA GLY GLU MET SEQRES 5 B 109 GLN ASP SER ILE VAL VAL VAL LYS VAL ASP VAL ASP GLU SEQRES 6 B 109 CYS GLU ASP ILE ALA THR GLU TYR ASN ILE ASN SER MET SEQRES 7 B 109 PRO THR PHE VAL PHE VAL LYS ASN GLY LYS LYS ILE GLU SEQRES 8 B 109 GLU PHE SER GLY ALA ASN VAL ASP LYS LEU ARG ASN THR SEQRES 9 B 109 ILE LEU LYS LEU LYS FORMUL 3 HOH *188(H2 O) HELIX 1 AA1 ASP A 7 ALA A 18 1 12 HELIX 2 AA2 CYS A 32 GLU A 48 1 17 HELIX 3 AA3 CYS A 63 TYR A 70 1 8 HELIX 4 AA4 ASN A 94 LYS A 106 1 13 HELIX 5 AA5 ASP B 7 ALA B 18 1 12 HELIX 6 AA6 CYS B 32 GLU B 48 1 17 HELIX 7 AA7 CYS B 63 TYR B 70 1 8 HELIX 8 AA8 ASN B 94 LYS B 106 1 13 SHEET 1 AA1 5 ILE A 3 HIS A 4 0 SHEET 2 AA1 5 ILE A 53 ASP A 59 1 O LYS A 57 N ILE A 3 SHEET 3 AA1 5 LEU A 22 MET A 28 1 N VAL A 24 O VAL A 54 SHEET 4 AA1 5 THR A 77 LYS A 82 -1 O VAL A 81 N VAL A 23 SHEET 5 AA1 5 LYS A 85 SER A 91 -1 O GLU A 88 N PHE A 80 SHEET 1 AA2 5 ILE B 3 HIS B 4 0 SHEET 2 AA2 5 ILE B 53 ASP B 59 1 O LYS B 57 N ILE B 3 SHEET 3 AA2 5 LEU B 22 MET B 28 1 N VAL B 24 O VAL B 54 SHEET 4 AA2 5 THR B 77 LYS B 82 -1 O VAL B 81 N VAL B 23 SHEET 5 AA2 5 LYS B 85 SER B 91 -1 O ILE B 87 N PHE B 80 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.05 SSBOND 2 CYS B 32 CYS B 35 1555 1555 2.04 CISPEP 1 MET A 75 PRO A 76 0 -4.89 CISPEP 2 MET B 75 PRO B 76 0 -6.96 CRYST1 107.710 28.980 79.860 90.00 128.32 90.00 C 1 2 1 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 0.009284 0.000000 0.007337 0.00000 SCALE2 0.000000 0.034507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015960 0.00000