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 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,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : 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 RCSB ID CODE IS RCSB071970. 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/DM/RESOLVE/HKL3000 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 MASTER 304 0 5 6 0 0 8 6 0 0 0 11 END