HEADER OXIDOREDUCTASE 09-APR-03 1UC7 TITLE CRYSTAL STRUCTURE OF DSBDGAMMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: DSBDGAMMA; COMPND 6 EC: 1.8.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS THIOREDOXIN-FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.KIM,S.J.KIM,D.G.JEONG,J.H.SON,S.E.RYU REVDAT 3 27-DEC-23 1UC7 1 REMARK REVDAT 2 24-FEB-09 1UC7 1 VERSN REVDAT 1 27-APR-04 1UC7 0 JRNL AUTH J.H.KIM,S.J.KIM,D.G.JEONG,J.H.SON,S.E.RYU JRNL TITL CRYSTAL STRUCTURE OF DSBDGAMMA REVEALS THE MECHANISM OF JRNL TITL 2 REDOX POTENTIAL SHIFT AND SUBSTRATE SPECIFICITY(1) JRNL REF FEBS LETT. V. 543 164 2003 JRNL REFN ISSN 0014-5793 JRNL PMID 12753926 JRNL DOI 10.1016/S0014-5793(03)00434-4 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17604 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RAMDOM REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 845 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 118 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-01; 13-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 298; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; PAL/PLS REMARK 200 BEAMLINE : NULL; 6B REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.9795, 0.9792, 0.9717 REMARK 200 MONOCHROMATOR : CONFOCAL; MIRRORS REMARK 200 OPTICS : MIRRORS; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17648 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEK 8000, SODIUM ACETATE, AMMONIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 15.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.83000 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 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 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 THR A 1 REMARK 465 THR B 1001 DBREF 1UC7 A 1 125 UNP P58162 DSBD_ECO57 441 565 DBREF 1UC7 B 1001 1125 UNP P58162 DSBD_ECO57 441 565 SEQRES 1 A 125 THR ALA GLN THR GLN THR HIS LEU ASN PHE THR GLN ILE SEQRES 2 A 125 LYS THR VAL ASP GLU LEU ASN GLN ALA LEU VAL GLU ALA SEQRES 3 A 125 LYS GLY LYS PRO VAL MET LEU ASP LEU TYR ALA ASP TRP SEQRES 4 A 125 CYS VAL ALA CYS LYS GLU PHE GLU LYS TYR THR PHE SER SEQRES 5 A 125 ASP PRO GLN VAL GLN LYS ALA LEU ALA ASP THR VAL LEU SEQRES 6 A 125 LEU GLN ALA ASN VAL THR ALA ASN ASP ALA GLN ASP VAL SEQRES 7 A 125 ALA LEU LEU LYS HIS LEU ASN VAL LEU GLY LEU PRO THR SEQRES 8 A 125 ILE LEU PHE PHE ASP GLY GLN GLY GLN GLU HIS PRO GLN SEQRES 9 A 125 ALA ARG VAL THR GLY PHE MET ASP ALA GLU THR PHE SER SEQRES 10 A 125 ALA HIS LEU ARG ASP ARG GLN PRO SEQRES 1 B 125 THR ALA GLN THR GLN THR HIS LEU ASN PHE THR GLN ILE SEQRES 2 B 125 LYS THR VAL ASP GLU LEU ASN GLN ALA LEU VAL GLU ALA SEQRES 3 B 125 LYS GLY LYS PRO VAL MET LEU ASP LEU TYR ALA ASP TRP SEQRES 4 B 125 CYS VAL ALA CYS LYS GLU PHE GLU LYS TYR THR PHE SER SEQRES 5 B 125 ASP PRO GLN VAL GLN LYS ALA LEU ALA ASP THR VAL LEU SEQRES 6 B 125 LEU GLN ALA ASN VAL THR ALA ASN ASP ALA GLN ASP VAL SEQRES 7 B 125 ALA LEU LEU LYS HIS LEU ASN VAL LEU GLY LEU PRO THR SEQRES 8 B 125 ILE LEU PHE PHE ASP GLY GLN GLY GLN GLU HIS PRO GLN SEQRES 9 B 125 ALA ARG VAL THR GLY PHE MET ASP ALA GLU THR PHE SER SEQRES 10 B 125 ALA HIS LEU ARG ASP ARG GLN PRO FORMUL 3 HOH *118(H2 O) HELIX 1 1 THR A 15 ALA A 26 1 12 HELIX 2 2 CYS A 40 THR A 50 1 11 HELIX 3 3 ASP A 53 LEU A 60 1 8 HELIX 4 4 ASP A 74 ASN A 85 1 12 HELIX 5 5 HIS A 102 ARG A 106 5 5 HELIX 6 6 ASP A 112 GLN A 124 1 13 HELIX 7 7 THR B 1015 ALA B 1026 1 12 HELIX 8 8 CYS B 1040 THR B 1050 1 11 HELIX 9 9 ASP B 1053 LEU B 1060 1 8 HELIX 10 10 ASP B 1074 LEU B 1084 1 11 HELIX 11 11 HIS B 1102 ARG B 1106 5 5 HELIX 12 12 ASP B 1112 ARG B 1123 1 12 SHEET 1 A 2 THR A 4 LEU A 8 0 SHEET 2 A 2 THR B1004 LEU B1008 -1 O HIS B1007 N GLN A 5 SHEET 1 B 4 THR A 11 GLN A 12 0 SHEET 2 B 4 VAL A 64 ASN A 69 1 O LEU A 65 N THR A 11 SHEET 3 B 4 VAL A 31 TYR A 36 1 N TYR A 36 O ALA A 68 SHEET 4 B 4 THR A 91 PHE A 95 -1 O PHE A 95 N VAL A 31 SHEET 1 C 4 THR B1011 GLN B1012 0 SHEET 2 C 4 VAL B1064 ASN B1069 1 O LEU B1065 N THR B1011 SHEET 3 C 4 VAL B1031 TYR B1036 1 N TYR B1036 O ALA B1068 SHEET 4 C 4 THR B1091 PHE B1095 -1 O LEU B1093 N LEU B1033 SSBOND 1 CYS A 40 CYS A 43 1555 1555 2.03 SSBOND 2 CYS B 1040 CYS B 1043 1555 1555 2.04 CISPEP 1 LEU A 89 PRO A 90 0 0.14 CISPEP 2 LEU B 1089 PRO B 1090 0 0.17 CRYST1 30.330 57.660 126.600 90.00 90.00 90.00 P 21 21 21 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 0.032971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007899 0.00000