HEADER TRANSFERASE 15-MAR-16 5IS1 TITLE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF SENSOR HISTIDINE TITLE 2 KINASE YYCG FROM STAPHYLOCOCCUS AUREUS AT 2.0 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAI, UNP RESIDUES 33-182; COMPND 5 SYNONYM: SENSOR HISTIDINE KINASE YYCG, PAS DOMAIN-CONTAINING SENSOR COMPND 6 HISTIDINE KINASE,TWO-COMPONENT SENSOR HISTIDINE KINASE,TWO-COMPONENT COMPND 7 SENSOR HISTIDINE KINASE (YYCG); COMPND 8 EC: 2.7.13.3; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: RN4220; SOURCE 5 GENE: WALK, WALK_1, AL493_01420, AL498_11610, AL508_14645, SOURCE 6 AM595_00105, ASU36_11995, AUC48_00105, AUC49_00105, AUC50_00105, SOURCE 7 BN1321_430109, CH51_00105, EQ80_000105, ER12_000105, SOURCE 8 ERS092844_02460, ERS093009_00906, ERS179246_01836, ERS195423_01765, SOURCE 9 ERS365775_01678, ERS410449_00558, ERS411009_01438, ERS411017_01103, SOURCE 10 ERS445051_00023, ERS445052_00659, FE68_05490, NI36_00110, SOURCE 11 RL02_04070, RT87_00105, SA7112_13655, SASCBU26_00023; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PAS/PDC DOMAIN, SENSOR HISTIDINE KINASE, NEST MOTIF, MEMBRANE KEYWDS 2 PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KIM,J.CHOI,S.LEE,K.K.KIM REVDAT 3 20-MAR-24 5IS1 1 JRNL REMARK REVDAT 2 17-AUG-16 5IS1 1 JRNL REVDAT 1 20-JUL-16 5IS1 0 JRNL AUTH T.KIM,J.CHOI,S.LEE,K.J.YEO,H.K.CHEONG,K.K.KIM JRNL TITL STRUCTURAL STUDIES ON THE EXTRACELLULAR DOMAIN OF SENSOR JRNL TITL 2 HISTIDINE KINASE YYCG FROM STAPHYLOCOCCUS AUREUS AND ITS JRNL TITL 3 FUNCTIONAL IMPLICATIONS JRNL REF J.MOL.BIOL. V. 428 3074 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27389096 JRNL DOI 10.1016/J.JMB.2016.06.019 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9749 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.110 REMARK 3 FREE R VALUE TEST SET COUNT : 986 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 19.8301 - 3.8146 0.96 1290 149 0.2306 0.2400 REMARK 3 2 3.8146 - 3.0312 1.00 1272 143 0.2084 0.2347 REMARK 3 3 3.0312 - 2.6491 1.00 1251 141 0.1856 0.2086 REMARK 3 4 2.6491 - 2.4073 1.00 1244 137 0.1732 0.2333 REMARK 3 5 2.4073 - 2.2350 1.00 1248 143 0.1588 0.2103 REMARK 3 6 2.2350 - 2.1034 1.00 1227 136 0.1471 0.1907 REMARK 3 7 2.1034 - 1.9982 1.00 1231 137 0.1303 0.1832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.014 1184 REMARK 3 ANGLE : 1.385 1594 REMARK 3 CHIRALITY : 0.079 178 REMARK 3 PLANARITY : 0.005 208 REMARK 3 DIHEDRAL : 15.770 461 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 5IS1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219344. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9779 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 71.3550 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40-55% (W/V) PEG 400, 100MM 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID (MES) PH 6.0, MICROBATCH, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 62.09667 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 31.04833 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 31.04833 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 62.09667 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: DIMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 25.30500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 43.82955 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 31.04833 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 269 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 270 LIES ON A SPECIAL POSITION. 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 GLY A 31 REMARK 465 SER A 32 REMARK 465 PHE A 33 REMARK 465 THR A 34 REMARK 465 VAL A 70 REMARK 465 ASN A 178 REMARK 465 ASN A 179 REMARK 465 ILE A 180 REMARK 465 ASN A 181 REMARK 465 GLN A 182 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 GLU A 66 -53.96 -130.12 REMARK 500 GLN A 99 31.63 72.06 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 275 DISTANCE = 8.19 ANGSTROMS DBREF 5IS1 A 33 182 UNP V5YQR2 V5YQR2_STAAU 33 182 SEQADV 5IS1 GLY A 31 UNP V5YQR2 EXPRESSION TAG SEQADV 5IS1 SER A 32 UNP V5YQR2 EXPRESSION TAG SEQRES 1 A 152 GLY SER PHE THR ASN ASN LEU GLU LYS GLU LEU LEU ASP SEQRES 2 A 152 ASN PHE LYS LYS ASN ILE THR GLN TYR ALA LYS GLN LEU SEQRES 3 A 152 GLU ILE SER ILE GLU LYS VAL TYR ASP GLU LYS GLY SER SEQRES 4 A 152 VAL ASN ALA GLN LYS ASP ILE GLN ASN LEU LEU SER GLU SEQRES 5 A 152 TYR ALA ASN ARG GLN GLU ILE GLY GLU ILE ARG PHE ILE SEQRES 6 A 152 ASP LYS ASP GLN ILE ILE ILE ALA THR THR LYS GLN SER SEQRES 7 A 152 ASN ARG SER LEU ILE ASN GLN LYS ALA ASN ASP SER SER SEQRES 8 A 152 VAL GLN LYS ALA LEU SER LEU GLY GLN SER ASN ASP HIS SEQRES 9 A 152 LEU ILE LEU LYS ASP TYR GLY GLY GLY LYS ASP ARG VAL SEQRES 10 A 152 TRP VAL TYR ASN ILE PRO VAL LYS VAL ASP LYS LYS VAL SEQRES 11 A 152 ILE GLY ASN ILE TYR ILE GLU SER LYS ILE ASN ASP VAL SEQRES 12 A 152 TYR ASN GLN LEU ASN ASN ILE ASN GLN FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 ASN A 36 GLU A 66 1 31 HELIX 2 AA2 ALA A 72 ALA A 84 1 13 HELIX 3 AA3 LYS A 106 ILE A 113 5 8 HELIX 4 AA4 ASP A 119 GLY A 129 1 11 HELIX 5 AA5 ILE A 170 LEU A 177 1 8 SHEET 1 AA1 5 ILE A 101 THR A 104 0 SHEET 2 AA1 5 ILE A 89 ASP A 96 -1 N PHE A 94 O ILE A 102 SHEET 3 AA1 5 LYS A 159 SER A 168 -1 O GLU A 167 N GLY A 90 SHEET 4 AA1 5 LYS A 144 VAL A 156 -1 N ILE A 152 O ILE A 164 SHEET 5 AA1 5 ASN A 132 ASP A 139 -1 N HIS A 134 O VAL A 149 CISPEP 1 GLY A 68 SER A 69 0 -9.18 CRYST1 50.610 50.610 93.145 90.00 90.00 120.00 P 32 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 0.019759 0.011408 0.000000 0.00000 SCALE2 0.000000 0.022816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010736 0.00000