10 20 30 40 50 60 70 80 2B1L - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 16-SEP-05 2B1L
TITLE CRYSTAL STRUCTURE OF N-TERMINAL 57 RESIDUE DELETION MUTANT TITLE 2 OF E. COLI CCMG PROTEIN(RESIDUES 58-185)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CCMG PROTEIN, CYTOCHROME C BIOGENESIS PROTEIN COMPND 5 CCMG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: N-TERMINAL 57 RESIDUE DELETION MUTANT
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 COMPARISON WITH THE E.COLI CCMG, FOLDING TOPOLOGY CHANGE, KEYWDS 2 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR N.OUYANG,Y.G.GAO,H.Y.HU,Z.X.XIA
REVDAT 4 24-FEB-09 2B1L 1 VERSN REVDAT 3 05-DEC-06 2B1L 1 JRNL AUTHOR REVDAT 2 12-SEP-06 2B1L 1 JRNL REVDAT 1 05-SEP-06 2B1L 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 JRNL TITL 2 REVEAL KEY ROLES OF THE N-TERMINAL BETA-SHEET AND JRNL TITL 3 THE FINGERPRINT REGION JRNL REF PROTEINS V. 65 1021 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17019698 JRNL DOI 10.1002/PROT.21184
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 29.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 285770.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 19228 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) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1891 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) (%) : 75.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1379 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 149 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2066 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.82000 REMARK 3 B22 (A**2) : -2.78000 REMARK 3 B33 (A**2) : -3.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.33000 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) : 0.26 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) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75 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) : 1.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.440 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 45.02 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 2B1L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-05. REMARK 100 THE RCSB ID CODE IS RCSB034561.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-05 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) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19846 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: STRUCTURE OF E.COLI CCMG REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES BUFFER, AMMONIUM SULFATE, PEG REMARK 280 4000, PH 7.8, SEEDING, TEMPERATURE 293.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.67450 REMARK 290 SMTRY3 2 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 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 TYR A 157 149.67 -170.74 REMARK 500 LYS B 106 52.47 39.76 REMARK 500 REMARK 500 REMARK: NULL
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 A 187 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH B 247 DISTANCE = 5.40 ANGSTROMS REMARK 525 HOH A 253 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 255 DISTANCE = 7.51 ANGSTROMS
DBREF 2B1L A 58 185 UNP P0AA86 DSBE_ECOLI 58 185 DBREF 2B1L B 58 185 UNP P0AA86 DSBE_ECOLI 58 185
SEQADV 2B1L MET A 57 UNP P0AA86 INITIATING METHIONINE SEQADV 2B1L MET B 57 UNP P0AA86 INITIATING METHIONINE
SEQRES 1 A 129 MET GLN PHE TYR GLN ALA ASP VAL LEU THR GLN GLY LYS SEQRES 2 A 129 PRO VAL LEU LEU ASN VAL TRP ALA THR TRP CYS PRO THR SEQRES 3 A 129 CYS ARG ALA GLU HIS GLN TYR LEU ASN GLN LEU SER ALA SEQRES 4 A 129 GLN GLY ILE ARG VAL VAL GLY MET ASN TYR LYS ASP ASP SEQRES 5 A 129 ARG GLN LYS ALA ILE SER TRP LEU LYS GLU LEU GLY ASN SEQRES 6 A 129 PRO TYR ALA LEU SER LEU PHE ASP GLY ASP GLY MET LEU SEQRES 7 A 129 GLY LEU ASP LEU GLY VAL TYR GLY ALA PRO GLU THR PHE SEQRES 8 A 129 LEU ILE ASP GLY ASN GLY ILE ILE ARG TYR ARG HIS ALA SEQRES 9 A 129 GLY ASP LEU ASN PRO ARG VAL TRP GLU GLU GLU ILE LYS SEQRES 10 A 129 PRO LEU TRP GLU LYS TYR SER LYS GLU ALA ALA GLN SEQRES 1 B 129 MET GLN PHE TYR GLN ALA ASP VAL LEU THR GLN GLY LYS SEQRES 2 B 129 PRO VAL LEU LEU ASN VAL TRP ALA THR TRP CYS PRO THR SEQRES 3 B 129 CYS ARG ALA GLU HIS GLN TYR LEU ASN GLN LEU SER ALA SEQRES 4 B 129 GLN GLY ILE ARG VAL VAL GLY MET ASN TYR LYS ASP ASP SEQRES 5 B 129 ARG GLN LYS ALA ILE SER TRP LEU LYS GLU LEU GLY ASN SEQRES 6 B 129 PRO TYR ALA LEU SER LEU PHE ASP GLY ASP GLY MET LEU SEQRES 7 B 129 GLY LEU ASP LEU GLY VAL TYR GLY ALA PRO GLU THR PHE SEQRES 8 B 129 LEU ILE ASP GLY ASN GLY ILE ILE ARG TYR ARG HIS ALA SEQRES 9 B 129 GLY ASP LEU ASN PRO ARG VAL TRP GLU GLU GLU ILE LYS SEQRES 10 B 129 PRO LEU TRP GLU LYS TYR SER LYS GLU ALA ALA GLN
FORMUL 3 HOH *139(H2 O)
HELIX 1 1 ALA A 62 GLN A 67 1 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 PRO A 165 ILE A 172 1 8 HELIX 5 5 ILE A 172 ALA A 184 1 13 HELIX 6 6 ALA B 62 GLN B 67 1 6 HELIX 7 7 THR B 82 GLY B 97 1 16 HELIX 8 8 ASP B 108 GLY B 120 1 13 HELIX 9 9 PRO B 165 ILE B 172 1 8 HELIX 10 10 ILE B 172 ALA B 184 1 13
SHEET 1 A 2 GLN A 58 ALA A 62 0 SHEET 2 A 2 GLY A 132 LEU A 134 1 O GLY A 132 N TYR A 60 SHEET 1 B 5 ALA A 124 ASP A 129 0 SHEET 2 B 5 ARG A 99 TYR A 105 1 N ASN A 104 O LEU A 127 SHEET 3 B 5 VAL A 71 TRP A 76 1 N ASN A 74 O VAL A 101 SHEET 4 B 5 PRO A 144 ASP A 150 -1 O GLU A 145 N VAL A 75 SHEET 5 B 5 ILE A 154 GLY A 161 -1 O HIS A 159 N THR A 146 SHEET 1 C 2 GLN B 58 ALA B 62 0 SHEET 2 C 2 GLY B 132 LEU B 134 1 O GLY B 132 N TYR B 60 SHEET 1 D 5 ALA B 124 ASP B 129 0 SHEET 2 D 5 ARG B 99 TYR B 105 1 N ASN B 104 O LEU B 127 SHEET 3 D 5 VAL B 71 TRP B 76 1 N ASN B 74 O VAL B 101 SHEET 4 D 5 PRO B 144 ASP B 150 -1 O GLU B 145 N VAL B 75 SHEET 5 D 5 ILE B 154 GLY B 161 -1 O HIS B 159 N THR B 146
SSBOND 1 CYS A 80 CYS A 83 1555 1555 2.03 SSBOND 2 CYS B 80 CYS B 83 1555 1555 2.04
CISPEP 1 ALA A 143 PRO A 144 0 -0.74 CISPEP 2 ALA B 143 PRO B 144 0 -0.59
CRYST1 37.691 43.349 78.986 90.00 94.94 90.00 P 1 21 1 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 0.026532 0.000000 0.002292 0.00000
SCALE2 0.000000 0.023069 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012708 0.00000