HEADER OXIDOREDUCTASE 14-OCT-09 3K8N TITLE CRYSTAL STRUCTURE OF E. COLI CCMG COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C BIOGENESIS PROTEIN CCMG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2195, CCMG, DSBE, JW2183, YEJQ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: LIC KEYWDS N-TERMINAL TRANSMEMBRANE HELIX, C-TERMINAL THIOREDOXIN-LIKE DOMAIN, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, CENTER FOR KEYWDS 3 STRUCTURES OF MEMBRANE PROTEINS, CSMP, CELL INNER MEMBRANE, CELL KEYWDS 4 MEMBRANE, CYTOCHROME C-TYPE BIOGENESIS, DISULFIDE BOND, MEMBRANE, KEYWDS 5 REDOX-ACTIVE CENTER, TRANSMEMBRANE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.SAVAGE,Z.NEWBY,R.M.STROUD,CENTER FOR STRUCTURES OF MEMBRANE AUTHOR 2 PROTEINS (CSMP) REVDAT 3 06-SEP-23 3K8N 1 REMARK REVDAT 2 01-NOV-17 3K8N 1 REMARK REVDAT 1 23-MAR-10 3K8N 0 JRNL AUTH D.SAVAGE,Z.NEWBY,R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF E. COLI CCMG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 62.1020 - 3.9330 0.99 2578 132 0.1780 0.1820 REMARK 3 2 3.9330 - 3.1220 1.00 2433 162 0.1960 0.2480 REMARK 3 3 3.1220 - 2.7270 1.00 2452 122 0.2600 0.3270 REMARK 3 4 2.7270 - 2.4780 1.00 2455 105 0.2810 0.3010 REMARK 3 5 2.4780 - 2.3000 0.98 2388 113 0.3370 0.3450 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 47.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1250 REMARK 3 ANGLE : 1.288 1700 REMARK 3 CHIRALITY : 0.082 178 REMARK 3 PLANARITY : 0.006 224 REMARK 3 DIHEDRAL : 20.803 454 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : KHOZU DOUBLE FLAT CRYSTAL REMARK 200 OPTICS : MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17017 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 62.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.560 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15200 REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.91700 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1KNG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS CONTAINED 1:1 REMARK 280 PROTEIN:PRECIPITANT, WHERE PRECIPITANT SOLUTION WAS 30% (W/V) REMARK 280 PEG 4000, 0.2M AMMONIUM SULFATE, PH 5.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.34800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.70150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.68700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.34800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.70150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.68700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.34800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.70150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.68700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.34800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.70150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.68700 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 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 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 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 ILE A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 ILE A 11 REMARK 465 ILE A 12 REMARK 465 PHE A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ILE A 16 REMARK 465 ALA A 17 REMARK 465 ALA 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 ALA A 184 REMARK 465 GLN A 185 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 181 CG CD CE NZ 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 LEU A 40 -10.44 78.48 REMARK 500 ASN A 104 107.18 -57.78 REMARK 500 LYS A 106 52.32 37.91 REMARK 500 GLU A 182 45.80 -78.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KNG RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CCMG FROM BRADYRHIZOBIUM JAPONICUM REMARK 900 RELATED ID: 2B1K RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CCMG FROM E. COLI REMARK 900 RELATED ID: 2461S RELATED DB: TARGETDB DBREF 3K8N A 1 185 UNP P0AA86 DSBE_ECOLI 1 185 SEQRES 1 A 185 MET LYS ARG LYS VAL LEU LEU ILE PRO LEU ILE ILE PHE SEQRES 2 A 185 LEU ALA ILE ALA ALA ALA LEU LEU TRP GLN LEU ALA ARG SEQRES 3 A 185 ASN ALA GLU GLY ASP ASP PRO THR ASN LEU GLU SER ALA SEQRES 4 A 185 LEU ILE GLY LYS PRO VAL PRO LYS PHE ARG LEU GLU SER SEQRES 5 A 185 LEU ASP ASN PRO GLY GLN PHE TYR GLN ALA ASP VAL LEU SEQRES 6 A 185 THR GLN GLY LYS PRO VAL LEU LEU ASN VAL TRP ALA THR SEQRES 7 A 185 TRP CYS PRO THR CYS ARG ALA GLU HIS GLN TYR LEU ASN SEQRES 8 A 185 GLN LEU SER ALA GLN GLY ILE ARG VAL VAL GLY MET ASN SEQRES 9 A 185 TYR LYS ASP ASP ARG GLN LYS ALA ILE SER TRP LEU LYS SEQRES 10 A 185 GLU LEU GLY ASN PRO TYR ALA LEU SER LEU PHE ASP GLY SEQRES 11 A 185 ASP GLY MET LEU GLY LEU ASP LEU GLY VAL TYR GLY ALA SEQRES 12 A 185 PRO GLU THR PHE LEU ILE ASP GLY ASN GLY ILE ILE ARG SEQRES 13 A 185 TYR ARG HIS ALA GLY ASP LEU ASN PRO ARG VAL TRP GLU SEQRES 14 A 185 GLU GLU ILE LYS PRO LEU TRP GLU LYS TYR SER LYS GLU SEQRES 15 A 185 ALA ALA GLN FORMUL 2 HOH *98(H2 O) HELIX 1 1 ASN A 35 ALA A 39 5 5 HELIX 2 2 ASP A 63 THR A 66 5 4 HELIX 3 3 THR A 82 GLN A 96 1 15 HELIX 4 4 ASP A 108 GLY A 120 1 13 HELIX 5 5 GLY A 132 LEU A 138 1 7 HELIX 6 6 ASN A 164 GLU A 171 1 8 HELIX 7 7 ILE A 172 LYS A 181 1 10 SHEET 1 A 2 ARG A 49 GLU A 51 0 SHEET 2 A 2 PHE A 59 GLN A 61 -1 O TYR A 60 N LEU A 50 SHEET 1 B 5 SER A 126 ASP A 129 0 SHEET 2 B 5 VAL A 100 TYR A 105 1 N GLY A 102 O LEU A 127 SHEET 3 B 5 VAL A 71 TRP A 76 1 N LEU A 72 O VAL A 101 SHEET 4 B 5 GLU A 145 ILE A 149 -1 O GLU A 145 N VAL A 75 SHEET 5 B 5 ILE A 155 ALA A 160 -1 O ARG A 156 N LEU A 148 SSBOND 1 CYS A 80 CYS A 83 1555 1555 2.08 CISPEP 1 ALA A 143 PRO A 144 0 -1.78 CRYST1 52.696 67.403 159.374 90.00 90.00 90.00 I 2 2 2 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 0.018977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006275 0.00000