HEADER OXIDOREDUCTASE 15-SEP-05 2B1K TITLE CRYSTAL STRUCTURE OF E. COLI CCMG PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 18-185; COMPND 5 SYNONYM: CCMG PROTEIN, CYTOCHROME C BIOGENESIS PROTEIN CCMG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CCMG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS C-TERMINAL THIOREDOXIN-LIKE DOMAIN, N-TERMINAL BETA-SHEET, KEYWDS 2 FINGERPRINT RIGION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.OUYANG,Y.G.GAO,H.Y.HU,Z.X.XIA REVDAT 5 25-OCT-23 2B1K 1 SEQADV REVDAT 4 24-FEB-09 2B1K 1 VERSN REVDAT 3 05-DEC-06 2B1K 1 JRNL AUTHOR REVDAT 2 12-SEP-06 2B1K 1 JRNL REVDAT 1 05-SEP-06 2B1K 0 JRNL AUTH N.OUYANG,Y.G.GAO,H.Y.HU,Z.X.XIA JRNL TITL CRYSTAL STRUCTURES OF E. COLI CCMG AND ITS MUTANTS REVEAL JRNL TITL 2 KEY ROLES OF THE N-TERMINAL BETA-SHEET AND THE FINGERPRINT JRNL TITL 3 REGION JRNL REF PROTEINS V. 65 1021 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17019698 JRNL DOI 10.1002/PROT.21184 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 324812.360 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 11430 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1178 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 906 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 109 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1187 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.53000 REMARK 3 B22 (A**2) : -2.83000 REMARK 3 B33 (A**2) : 1.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 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) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.470 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.870 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 44.60 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.8 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 : CONVENTIONAL CU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER APEX REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12145 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1KNG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES BUFFER, AMMONIUM SULFATE, PEG REMARK 280 4000, PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 17.74150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.38750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.25750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.38750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.74150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.25750 REMARK 290 SMTRY3 4 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 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 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 MET A 18 REMARK 465 ALA A 19 REMARK 465 LEU A 20 REMARK 465 LEU A 21 REMARK 465 TRP A 22 REMARK 465 GLN A 23 REMARK 465 LEU A 24 REMARK 465 ALA A 25 REMARK 465 ARG A 26 REMARK 465 ASN A 27 REMARK 465 ALA A 28 REMARK 465 GLU A 29 REMARK 465 GLY A 30 REMARK 465 ASP A 31 REMARK 465 ASP A 32 REMARK 465 PRO A 33 REMARK 465 THR A 34 REMARK 465 ASN A 35 REMARK 465 GLN A 185 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 A 66 78.26 -112.42 REMARK 500 LYS A 106 59.20 34.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 2B1K A 19 185 UNP P0AA86 DSBE_ECOLI 19 185 SEQADV 2B1K MET A 18 UNP P0AA86 INITIATING METHIONINE SEQRES 1 A 168 MET ALA LEU LEU TRP GLN LEU ALA ARG ASN ALA GLU GLY SEQRES 2 A 168 ASP ASP PRO THR ASN LEU GLU SER ALA LEU ILE GLY LYS SEQRES 3 A 168 PRO VAL PRO LYS PHE ARG LEU GLU SER LEU ASP ASN PRO SEQRES 4 A 168 GLY GLN PHE TYR GLN ALA ASP VAL LEU THR GLN GLY LYS SEQRES 5 A 168 PRO VAL LEU LEU ASN VAL TRP ALA THR TRP CYS PRO THR SEQRES 6 A 168 CYS ARG ALA GLU HIS GLN TYR LEU ASN GLN LEU SER ALA SEQRES 7 A 168 GLN GLY ILE ARG VAL VAL GLY MET ASN TYR LYS ASP ASP SEQRES 8 A 168 ARG GLN LYS ALA ILE SER TRP LEU LYS GLU LEU GLY ASN SEQRES 9 A 168 PRO TYR ALA LEU SER LEU PHE ASP GLY ASP GLY MET LEU SEQRES 10 A 168 GLY LEU ASP LEU GLY VAL TYR GLY ALA PRO GLU THR PHE SEQRES 11 A 168 LEU ILE ASP GLY ASN GLY ILE ILE ARG TYR ARG HIS ALA SEQRES 12 A 168 GLY ASP LEU ASN PRO ARG VAL TRP GLU GLU GLU ILE LYS SEQRES 13 A 168 PRO LEU TRP GLU LYS TYR SER LYS GLU ALA ALA GLN FORMUL 2 HOH *63(H2 O) HELIX 1 1 GLN A 61 THR A 66 5 6 HELIX 2 2 THR A 82 GLY A 97 1 16 HELIX 3 3 ASP A 108 GLY A 120 1 13 HELIX 4 4 GLY A 132 GLY A 139 1 8 HELIX 5 5 PRO A 165 ILE A 172 1 8 HELIX 6 6 ILE A 172 ALA A 184 1 13 SHEET 1 A 7 GLN A 58 TYR A 60 0 SHEET 2 A 7 LEU A 50 SER A 52 -1 N LEU A 50 O TYR A 60 SHEET 3 A 7 ALA A 124 ASP A 129 -1 N PHE A 128 O GLU A 51 SHEET 4 A 7 ARG A 99 TYR A 105 1 O GLY A 102 N LEU A 127 SHEET 5 A 7 VAL A 71 TRP A 76 1 O LEU A 72 N VAL A 101 SHEET 6 A 7 PRO A 144 ASP A 150 -1 O GLU A 145 N VAL A 75 SHEET 7 A 7 ILE A 154 GLY A 161 -1 O TYR A 157 N LEU A 148 SSBOND 1 CYS A 80 CYS A 83 1555 1555 2.02 CISPEP 1 ALA A 143 PRO A 144 0 0.05 CRYST1 35.483 48.515 84.775 90.00 90.00 90.00 P 21 21 21 4 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 0.028183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011796 0.00000