HEADER TRANSFERASE 28-AUG-12 4GT8 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC AND ATP-BINDING DOMAIN FROM VRAS IN TITLE 2 COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN VRAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC AND ATP-BINDING DOMAIN; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50 / ATCC 700699; SOURCE 5 GENE: SAV1885, VRAS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) T1R; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P535 KEYWDS HISTIDINE KINASE, ATP HYDROLYSIS, TWO-COMPONENT SYSTEM, BACTERIAL KEYWDS 2 SIGNALLING, KINASE, ATP-BINDING, PHOSPHORYLATION, MEMBRANE, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.G.LEONARD,J.VALVERDE,A.M.STOCK REVDAT 2 28-FEB-24 4GT8 1 REMARK SEQADV LINK REVDAT 1 28-AUG-13 4GT8 0 JRNL AUTH P.G.LEONARD,J.VALVERDE,A.M.STOCK JRNL TITL STRUCTURE OF THE STAPHYLOCOCCUS AUREUS VRAS CATALYTIC AND JRNL TITL 2 ATP-BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1066 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 19830 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1005 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 29.4564 - 2.8849 0.99 3073 163 0.1661 0.1657 REMARK 3 2 2.8849 - 2.2901 0.98 2884 152 0.1822 0.2024 REMARK 3 3 2.2901 - 2.0007 0.97 2835 152 0.1673 0.2058 REMARK 3 4 2.0007 - 1.8178 0.92 2644 146 0.1859 0.2093 REMARK 3 5 1.8178 - 1.6875 0.89 2565 135 0.2153 0.2657 REMARK 3 6 1.6875 - 1.5880 0.87 2505 130 0.2398 0.2370 REMARK 3 7 1.5880 - 1.5100 0.81 2319 127 0.2852 0.3284 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.09 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 : 0.007 1136 REMARK 3 ANGLE : 1.208 1546 REMARK 3 CHIRALITY : 0.072 175 REMARK 3 PLANARITY : 0.004 194 REMARK 3 DIHEDRAL : 14.913 450 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 4GT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91810 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21323 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.98800 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 450 MM MGCL2, 30% REMARK 280 (W/V) PEG 3350, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.59600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.69900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.61650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.69900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.59600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.61650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 GLU A 342 REMARK 465 ASP A 343 REMARK 465 SER A 344 REMARK 465 TYR A 345 REMARK 465 ASP A 346 REMARK 465 ASP A 347 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 LYS A 213 -106.71 50.98 REMARK 500 ASP A 281 -68.81 68.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 259 OE2 REMARK 620 2 ASN A 263 OD1 89.4 REMARK 620 3 ADP A 401 O2A 86.7 88.6 REMARK 620 4 ADP A 401 O3B 175.5 91.0 88.8 REMARK 620 5 HOH A 574 O 86.6 86.9 172.0 97.9 REMARK 620 6 HOH A 576 O 89.2 176.3 94.7 90.7 89.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 DBREF 4GT8 A 212 347 UNP Q7A2Q0 VRAS_STAAM 212 347 SEQADV 4GT8 GLY A 209 UNP Q7A2Q0 EXPRESSION TAG SEQADV 4GT8 ALA A 210 UNP Q7A2Q0 EXPRESSION TAG SEQADV 4GT8 MET A 211 UNP Q7A2Q0 EXPRESSION TAG SEQRES 1 A 139 GLY ALA MET LEU LYS ASP LYS SER LEU GLY GLU GLY ILE SEQRES 2 A 139 LYS ASP LEU VAL ILE ASP LEU GLN LYS LYS VAL PRO MET SEQRES 3 A 139 LYS VAL VAL HIS GLU ILE GLN ASP PHE LYS VAL PRO LYS SEQRES 4 A 139 GLY ILE GLU ASP HIS LEU PHE ARG ILE THR GLN GLU ALA SEQRES 5 A 139 ILE SER ASN THR LEU ARG HIS SER ASN GLY THR LYS VAL SEQRES 6 A 139 THR VAL GLU LEU PHE ASN LYS ASP ASP TYR LEU LEU LEU SEQRES 7 A 139 ARG ILE GLN ASP ASN GLY LYS GLY PHE ASN VAL ASP GLU SEQRES 8 A 139 LYS LEU GLU GLN SER TYR GLY LEU LYS ASN MET ARG GLU SEQRES 9 A 139 ARG ALA LEU GLU ILE GLY ALA THR PHE HIS ILE VAL SER SEQRES 10 A 139 LEU PRO ASP SER GLY THR ARG ILE GLU VAL LYS ALA PRO SEQRES 11 A 139 LEU ASN LYS GLU ASP SER TYR ASP ASP HET ADP A 401 27 HET MG A 402 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *136(H2 O) HELIX 1 1 SER A 216 LYS A 230 1 15 HELIX 2 2 PRO A 246 SER A 268 1 23 HELIX 3 3 ASN A 296 LEU A 301 1 6 HELIX 4 4 SER A 304 ILE A 317 1 14 SHEET 1 A 5 LYS A 235 ILE A 240 0 SHEET 2 A 5 LYS A 272 ASN A 279 1 O VAL A 275 N GLU A 239 SHEET 3 A 5 TYR A 283 ASP A 290 -1 O ARG A 287 N GLU A 276 SHEET 4 A 5 GLY A 330 PRO A 338 -1 O VAL A 335 N LEU A 286 SHEET 5 A 5 THR A 320 LEU A 326 -1 N VAL A 324 O ARG A 332 LINK OE2 GLU A 259 MG MG A 402 1555 1555 2.04 LINK OD1 ASN A 263 MG MG A 402 1555 1555 2.05 LINK O2A ADP A 401 MG MG A 402 1555 1555 1.95 LINK O3B ADP A 401 MG MG A 402 1555 1555 2.07 LINK MG MG A 402 O HOH A 574 1555 1555 2.07 LINK MG MG A 402 O HOH A 576 1555 1555 2.07 SITE 1 AC1 25 GLU A 259 ASN A 263 THR A 264 ARG A 266 SITE 2 AC1 25 HIS A 267 SER A 268 ASP A 290 PHE A 295 SITE 3 AC1 25 LYS A 300 SER A 304 TYR A 305 GLY A 306 SITE 4 AC1 25 LEU A 307 THR A 331 MG A 402 HOH A 502 SITE 5 AC1 25 HOH A 503 HOH A 505 HOH A 528 HOH A 576 SITE 6 AC1 25 HOH A 582 HOH A 589 HOH A 602 HOH A 605 SITE 7 AC1 25 HOH A 629 SITE 1 AC2 5 GLU A 259 ASN A 263 ADP A 401 HOH A 574 SITE 2 AC2 5 HOH A 576 CRYST1 31.192 47.233 89.398 90.00 90.00 90.00 P 21 21 21 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 0.032060 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011186 0.00000