HEADER ELECTRON TRANSPORT 15-NOV-01 1KEB TITLE CRYSTAL STRUCTURE OF DOUBLE MUTANT M37L,P40S E.COLI THIOREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRX; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET20BP40S KEYWDS THIOREDOXIN FOLD, PROLINE, ALPHA-HELIX, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR RUDRESH,R.JAIN,V.DANI,A.MITRA,S.SRIVASTAVA,S.P.SARMA,R.VARADARAJAN, AUTHOR 2 S.RAMAKUMAR REVDAT 4 16-AUG-23 1KEB 1 REMARK REVDAT 3 27-OCT-21 1KEB 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1KEB 1 VERSN REVDAT 1 13-NOV-02 1KEB 0 JRNL AUTH RUDRESH,R.JAIN,V.DANI,A.MITRA,S.SRIVASTAVA,S.P.SARMA, JRNL AUTH 2 R.VARADARAJAN,S.RAMAKUMAR JRNL TITL STRUCTURAL CONSEQUENCES OF REPLACEMENT OF AN ALPHA-HELICAL JRNL TITL 2 PRO RESIDUE IN E.COLI THIOREDOXIN JRNL REF PROTEIN ENG. V. 15 627 2002 JRNL REFN ISSN 0269-2139 JRNL PMID 12364576 JRNL DOI 10.1093/PROTEIN/15.8.627 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 73.5 REMARK 3 NUMBER OF REFLECTIONS : 13549 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1356 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2027 REMARK 3 BIN FREE R VALUE : 0.2452 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 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 : 1642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 2.27000 REMARK 3 B33 (A**2) : -2.26000 REMARK 3 B12 (A**2) : -0.12000 REMARK 3 B13 (A**2) : 0.40000 REMARK 3 B23 (A**2) : 1.05000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1KEB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 3.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, AUTOMAR REMARK 200 DATA SCALING SOFTWARE : MARSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16633 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36400 REMARK 200 FOR SHELL : 1.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2TRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE BUFFER, 10MM REMARK 280 CUPRIC ACETATE, 25% ETHANOL AS PRECIPITANT, PH 3.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 300K 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, 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 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 THR B 14 -63.10 -103.44 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 CU A 109 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 1 N REMARK 620 2 ASP A 2 N 81.7 REMARK 620 3 ASP A 2 OD1 171.1 89.4 REMARK 620 4 HOH A 159 O 84.3 81.5 94.1 REMARK 620 5 HIS B 6 ND1 95.3 175.2 93.6 94.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 109 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 SER B 1 N 95.4 REMARK 620 3 ASP B 2 N 177.5 84.3 REMARK 620 4 ASP B 2 OD1 87.6 177.0 92.7 REMARK 620 5 HOH B 154 O 87.2 92.5 90.4 87.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 109 DBREF 1KEB A 1 108 UNP P0AA25 THIO_ECOLI 1 108 DBREF 1KEB B 1 108 UNP P0AA25 THIO_ECOLI 1 108 SEQADV 1KEB LEU A 37 UNP P0AA25 MET 37 ENGINEERED MUTATION SEQADV 1KEB SER A 40 UNP P0AA25 PRO 40 ENGINEERED MUTATION SEQADV 1KEB LEU B 37 UNP P0AA25 MET 37 ENGINEERED MUTATION SEQADV 1KEB SER B 40 UNP P0AA25 PRO 40 ENGINEERED MUTATION SEQRES 1 A 108 SER ASP LYS ILE ILE HIS LEU THR ASP ASP SER PHE ASP SEQRES 2 A 108 THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL ASP SEQRES 3 A 108 PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS LEU ILE ALA SEQRES 4 A 108 SER ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY LYS SEQRES 5 A 108 LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO GLY SEQRES 6 A 108 THR ALA PRO LYS TYR GLY ILE ARG GLY ILE PRO THR LEU SEQRES 7 A 108 LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS VAL SEQRES 8 A 108 GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU ASP SEQRES 9 A 108 ALA ASN LEU ALA SEQRES 1 B 108 SER ASP LYS ILE ILE HIS LEU THR ASP ASP SER PHE ASP SEQRES 2 B 108 THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL ASP SEQRES 3 B 108 PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS LEU ILE ALA SEQRES 4 B 108 SER ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY LYS SEQRES 5 B 108 LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO GLY SEQRES 6 B 108 THR ALA PRO LYS TYR GLY ILE ARG GLY ILE PRO THR LEU SEQRES 7 B 108 LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS VAL SEQRES 8 B 108 GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU ASP SEQRES 9 B 108 ALA ASN LEU ALA HET CU A 109 1 HET CU B 109 1 HETNAM CU COPPER (II) ION FORMUL 3 CU 2(CU 2+) FORMUL 5 HOH *133(H2 O) HELIX 1 1 SER A 11 VAL A 16 1 6 HELIX 2 2 CYS A 32 SER A 40 1 9 HELIX 3 3 ILE A 41 TYR A 49 1 9 HELIX 4 4 THR A 66 GLY A 71 5 6 HELIX 5 5 SER A 95 LEU A 107 1 13 HELIX 6 6 THR B 8 VAL B 16 1 9 HELIX 7 7 CYS B 32 SER B 40 1 9 HELIX 8 8 ILE B 41 TYR B 49 1 9 HELIX 9 9 THR B 66 GLY B 71 5 6 HELIX 10 10 SER B 95 ALA B 108 1 14 SHEET 1 A 5 ILE A 4 HIS A 6 0 SHEET 2 A 5 THR A 54 ASN A 59 1 O LYS A 57 N ILE A 5 SHEET 3 A 5 ALA A 22 TRP A 28 1 N LEU A 24 O ALA A 56 SHEET 4 A 5 THR A 77 LYS A 82 -1 O LEU A 79 N VAL A 25 SHEET 5 A 5 GLU A 85 VAL A 91 -1 O ALA A 87 N LEU A 80 SHEET 1 B 5 ILE B 4 HIS B 6 0 SHEET 2 B 5 THR B 54 ASN B 59 1 O LYS B 57 N ILE B 5 SHEET 3 B 5 ALA B 22 TRP B 28 1 N LEU B 24 O ALA B 56 SHEET 4 B 5 THR B 77 LYS B 82 -1 O LEU B 79 N VAL B 25 SHEET 5 B 5 GLU B 85 VAL B 91 -1 O ALA B 87 N LEU B 80 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.03 SSBOND 2 CYS B 32 CYS B 35 1555 1555 2.03 LINK N SER A 1 CU CU A 109 1555 1555 2.05 LINK N ASP A 2 CU CU A 109 1555 1555 2.06 LINK OD1 ASP A 2 CU CU A 109 1555 1555 1.92 LINK OD1 ASP A 10 CU CU B 109 1555 1555 2.02 LINK CU CU A 109 O HOH A 159 1555 1555 2.51 LINK CU CU A 109 ND1 HIS B 6 1555 1545 2.13 LINK N SER B 1 CU CU B 109 1555 1555 2.03 LINK N ASP B 2 CU CU B 109 1555 1555 1.99 LINK OD1 ASP B 2 CU CU B 109 1555 1555 1.98 LINK CU CU B 109 O HOH B 154 1555 1555 2.65 CISPEP 1 ILE A 75 PRO A 76 0 0.37 CISPEP 2 ILE B 75 PRO B 76 0 0.23 SITE 1 AC1 4 SER A 1 ASP A 2 HOH A 159 HIS B 6 SITE 1 AC2 4 ASP A 10 SER B 1 ASP B 2 HOH B 154 CRYST1 29.320 37.500 50.740 69.25 79.71 85.39 P 1 2 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 0.034106 -0.002750 -0.005585 0.00000 SCALE2 0.000000 0.026753 -0.009886 0.00000 SCALE3 0.000000 0.000000 0.021354 0.00000