HEADER ELECTRON TRANSPORT 19-APR-12 4ER9 TITLE CRYSTAL STRUCTURE OF CYTOCHROME B562 FROM SALMONELLA ENTERICA SUBSP. TITLE 2 ENTERICA SEROVAR TYPHIMURIUM STR. 14028S COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 90371; SOURCE 5 STRAIN: 14028S; SOURCE 6 GENE: CYBC, STM4439; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, PROGRAM FOR THE KEYWDS 3 CHARACTERIZATION OF SECRETED EFFECTOR PROTEINS, PCSEP, ELECTRON KEYWDS 4 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,C.HATZOS-SKINTGES,R.JEDRZEJCZAK,J.ADKINS,A.JOACHIMIAK,MIDWEST AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (MCSG),PROGRAM FOR THE AUTHOR 3 CHARACTERIZATION OF SECRETED EFFECTOR PROTEINS (PCSEP) REVDAT 2 28-FEB-24 4ER9 1 REMARK SEQADV REVDAT 1 09-MAY-12 4ER9 0 JRNL AUTH K.TAN,C.HATZOS-SKINTGES,R.JEDRZEJCZAK,J.ADKINS,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF CYTOCHROME B562 FROM SALMONELLA JRNL TITL 2 ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. 14028S JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 11888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 570 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 40.8558 - 3.0113 0.98 2971 142 0.2075 0.2256 REMARK 3 2 3.0113 - 2.3903 1.00 2882 150 0.2401 0.3092 REMARK 3 3 2.3903 - 2.0881 1.00 2883 146 0.2479 0.3154 REMARK 3 4 2.0881 - 1.8972 0.91 2582 132 0.3037 0.3853 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 : 0.36 REMARK 3 B_SOL : 54.01 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.370 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) : -12.75360 REMARK 3 B22 (A**2) : -12.75360 REMARK 3 B33 (A**2) : 25.50720 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 : 0.007 838 REMARK 3 ANGLE : 0.993 1125 REMARK 3 CHIRALITY : 0.057 125 REMARK 3 PLANARITY : 0.005 145 REMARK 3 DIHEDRAL : 17.129 323 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 23:44) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7762 16.1883 15.8308 REMARK 3 T TENSOR REMARK 3 T11: 0.7049 T22: 0.6537 REMARK 3 T33: 0.3966 T12: 0.1354 REMARK 3 T13: 0.1604 T23: 0.1842 REMARK 3 L TENSOR REMARK 3 L11: 8.5506 L22: 8.0944 REMARK 3 L33: 5.0798 L12: -1.9547 REMARK 3 L13: 0.4252 L23: 0.6855 REMARK 3 S TENSOR REMARK 3 S11: 0.0367 S12: -1.0164 S13: -0.4566 REMARK 3 S21: 0.6350 S22: 0.2828 S23: 0.8384 REMARK 3 S31: 0.2190 S32: -0.8977 S33: -0.3283 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 45:102) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9606 13.9675 6.2318 REMARK 3 T TENSOR REMARK 3 T11: 0.2815 T22: 0.2119 REMARK 3 T33: 0.3553 T12: 0.0885 REMARK 3 T13: -0.0939 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 5.3238 L22: 6.5629 REMARK 3 L33: 3.2680 L12: -1.3378 REMARK 3 L13: 3.3356 L23: -1.0606 REMARK 3 S TENSOR REMARK 3 S11: 0.3479 S12: 0.0995 S13: -0.5663 REMARK 3 S21: 0.2862 S22: 0.0617 S23: -0.5672 REMARK 3 S31: 0.5379 S32: 0.2038 S33: -0.1752 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 103:127) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4537 17.7699 5.0387 REMARK 3 T TENSOR REMARK 3 T11: 0.3246 T22: 0.5136 REMARK 3 T33: 0.5138 T12: -0.0107 REMARK 3 T13: -0.0691 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 7.7752 L22: 8.0490 REMARK 3 L33: 5.4233 L12: 0.1687 REMARK 3 L13: 1.2709 L23: 1.9654 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.2034 S13: -0.9623 REMARK 3 S21: 0.5171 S22: 0.1385 S23: 0.2410 REMARK 3 S31: 0.5377 S32: -0.4637 S33: -0.0380 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 4ER9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97909 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11910 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 54.8000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, MLPHARE, HKL-3000, DM, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M AMMONIUM SULFATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.06300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.12600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.12600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.06300 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 300 REMARK: EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE MONOMERIC. 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 LYS A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 ALA A 7 REMARK 465 ILE A 8 REMARK 465 LEU A 9 REMARK 465 ALA A 10 REMARK 465 VAL A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PHE A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 ALA A 19 REMARK 465 VAL A 20 REMARK 465 PHE A 21 REMARK 465 ALA A 22 REMARK 465 ARG A 128 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MCSG-APC101501 RELATED DB: TARGETTRACK DBREF 4ER9 A 1 128 UNP P63727 C562_SALTY 1 128 SEQADV 4ER9 SER A -2 UNP P63727 EXPRESSION TAG SEQADV 4ER9 ASN A -1 UNP P63727 EXPRESSION TAG SEQADV 4ER9 ALA A 0 UNP P63727 EXPRESSION TAG SEQRES 1 A 131 SER ASN ALA MET ARG LYS SER LEU LEU ALA ILE LEU ALA SEQRES 2 A 131 VAL SER SER LEU VAL PHE GLY SER ALA VAL PHE ALA ALA SEQRES 3 A 131 ASP LEU GLU ASP ASN MET ASP ILE LEU ASN ASP ASN LEU SEQRES 4 A 131 LYS VAL VAL GLU LYS THR ASP SER ALA PRO GLU LEU LYS SEQRES 5 A 131 ALA ALA LEU THR LYS MET ARG ALA ALA ALA LEU ASP ALA SEQRES 6 A 131 GLN LYS ALA THR PRO PRO LYS LEU GLU ASP LYS ALA PRO SEQRES 7 A 131 ASP SER PRO GLU MET LYS ASP PHE ARG HIS GLY PHE ASP SEQRES 8 A 131 ILE LEU VAL GLY GLN ILE ASP GLY ALA LEU LYS LEU ALA SEQRES 9 A 131 ASN GLU GLY ASN VAL LYS GLU ALA LYS ALA ALA ALA GLU SEQRES 10 A 131 ALA LEU LYS THR THR ARG ASN THR TYR HIS LYS LYS TYR SEQRES 11 A 131 ARG HET PEG A 201 7 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET GOL A 205 6 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PEG C4 H10 O3 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *29(H2 O) HELIX 1 1 ALA A 23 THR A 42 1 20 HELIX 2 2 SER A 44 GLN A 63 1 20 HELIX 3 3 PRO A 67 GLU A 71 5 5 HELIX 4 4 SER A 77 GLU A 103 1 27 HELIX 5 5 ASN A 105 GLU A 114 1 10 HELIX 6 6 ALA A 115 LYS A 126 1 12 SITE 1 AC1 6 LYS A 64 GLY A 104 VAL A 106 LYS A 107 SITE 2 AC1 6 SO4 A 204 HOH A 310 SITE 1 AC2 1 ARG A 56 SITE 1 AC3 2 LYS A 81 ARG A 84 SITE 1 AC4 6 THR A 42 ASP A 43 LEU A 48 VAL A 106 SITE 2 AC4 6 LYS A 107 PEG A 201 SITE 1 AC5 6 MET A 29 PHE A 83 PHE A 87 TYR A 123 SITE 2 AC5 6 HIS A 124 TYR A 127 CRYST1 67.388 67.388 57.189 90.00 90.00 120.00 P 31 2 1 6 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 0.014839 0.008568 0.000000 0.00000 SCALE2 0.000000 0.017135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017486 0.00000