HEADER SIGNALING PROTEIN 02-AUG-22 8DWZ TITLE CA DOMAIN OF VANSA HISTIDINE KINASE, 7 KEV DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN VANS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VANCOMYCIN HISTIDINE PROTEIN KINASE,VANCOMYCIN RESISTANCE COMPND 5 PROTEIN VANS; COMPND 6 EC: 2.7.13.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS; SOURCE 3 ORGANISM_TAXID: 1350; SOURCE 4 GENE: VANS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ATP-BINDING, HISTIDINE KINASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.J.LOLL REVDAT 1 22-MAR-23 8DWZ 0 JRNL AUTH K.C.GRASTY,C.GUZIK,E.J.D'LAURO,S.B.PADRICK,J.BELD,P.J.LOLL JRNL TITL STRUCTURE OF VANS FROM VANCOMYCIN-RESISTANT ENTEROCOCCI: A JRNL TITL 2 SENSOR KINASE WITH WEAK ATP BINDING. JRNL REF J.BIOL.CHEM. V. 299 03001 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36764524 JRNL DOI 10.1016/J.JBC.2023.103001 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 17544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 911 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 56.1400 - 4.2400 0.99 2525 137 0.1541 0.1966 REMARK 3 2 4.2400 - 3.3600 0.99 2535 137 0.1819 0.2101 REMARK 3 3 3.3600 - 2.9400 0.98 2511 128 0.1969 0.2738 REMARK 3 4 2.9400 - 2.6700 0.97 2497 137 0.1988 0.2489 REMARK 3 5 2.6700 - 2.4800 0.96 2441 125 0.2075 0.2881 REMARK 3 6 2.4800 - 2.3300 0.93 2415 149 0.2203 0.2954 REMARK 3 7 2.3300 - 2.2100 0.67 1709 98 0.2685 0.3471 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) : 0.288 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.549 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.65 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 1024 REMARK 3 ANGLE : 0.793 1389 REMARK 3 CHIRALITY : 0.058 161 REMARK 3 PLANARITY : 0.005 180 REMARK 3 DIHEDRAL : 3.183 612 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 228:375 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.608 15.229 12.985 REMARK 3 T TENSOR REMARK 3 T11: 0.3411 T22: 0.3833 REMARK 3 T33: 0.3202 T12: 0.0013 REMARK 3 T13: -0.0199 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 5.3411 L22: 1.2201 REMARK 3 L33: 4.7956 L12: -0.0419 REMARK 3 L13: -1.3073 L23: 0.0166 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: 0.0777 S13: -0.2135 REMARK 3 S21: 0.0268 S22: 0.0552 S23: 0.0529 REMARK 3 S31: 0.1570 S32: -0.0869 S33: -0.0361 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 8DWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267509. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.7712 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 56.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 18.40 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57800 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: SAD 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 (%): 54.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VANSA CA DOMAIN PROTEIN WAS AT A REMARK 280 CONCENTRATION OF 2.5 MG/ML IN 20 MM TRIS PH 7.8, 150 MM NACL, REMARK 280 SUPPLEMENTED WITH 2.5 MM AMP-PNP AND 5 MM MGCL2. PROTEIN AND REMARK 280 PRECIPITANT WERE MIXED IN A VOLUME RATIO OF 1:2 AND INCUBATED REMARK 280 UNDER ALS OIL AT 291 K; THE PRECIPITANT SOLUTION CONTAINED 75 MM REMARK 280 BIS-TRIS PROPANE, 25 MM CITRIC ACID, PH 8.2, 20 MM CDCL2, AND 25% REMARK 280 (W/V) PEG 400., MICROBATCH REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 34.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.91500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.20000 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 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 ASN A 219 REMARK 465 LEU A 220 REMARK 465 GLN A 221 REMARK 465 THR A 222 REMARK 465 ILE A 223 REMARK 465 THR A 224 REMARK 465 LEU A 225 REMARK 465 THR A 226 REMARK 465 LYS A 227 REMARK 465 GLU A 323 REMARK 465 LYS A 324 REMARK 465 PHE A 325 REMARK 465 TYR A 326 REMARK 465 ARG A 327 REMARK 465 LEU A 328 REMARK 465 ASP A 329 REMARK 465 ASN A 330 REMARK 465 ALA A 331 REMARK 465 ARG A 332 REMARK 465 SER A 333 REMARK 465 SER A 334 REMARK 465 ASP A 335 REMARK 465 THR A 336 REMARK 465 GLY A 337 REMARK 465 GLY A 338 REMARK 465 ALA A 339 REMARK 465 PRO A 376 REMARK 465 ASP A 377 REMARK 465 LEU A 378 REMARK 465 VAL A 379 REMARK 465 ASP A 380 REMARK 465 LYS A 381 REMARK 465 ARG A 382 REMARK 465 ARG A 383 REMARK 465 SER A 384 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 CD A 401 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 229 NE2 REMARK 620 2 ASP A 231 OD1 91.7 REMARK 620 3 ASP A 231 OD2 93.2 55.9 REMARK 620 4 HIS A 250 ND1 99.8 29.4 28.2 REMARK 620 5 ASP A 288 OD1 99.5 24.1 33.4 5.4 REMARK 620 6 ASP A 288 OD2 100.4 24.1 33.8 5.7 1.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 402 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 257 ND1 REMARK 620 2 ASP A 267 OD1 53.9 REMARK 620 3 ASP A 267 OD2 52.6 2.5 REMARK 620 4 ASP A 269 OD1 55.5 5.4 7.8 REMARK 620 5 ASP A 269 OD2 51.2 6.1 7.6 4.4 REMARK 620 6 HOH A 521 O 117.7 70.9 71.0 72.3 76.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DVQ RELATED DB: PDB REMARK 900 8DVQ CONTAINS THE SAME PROTEIN, SAME CRYSTAL FORM, COLLECTED AT A REMARK 900 DIFFERENT WAVELENGTH DBREF 8DWZ A 219 384 UNP Q06240 VANS_ENTFC 219 384 SEQRES 1 A 166 ASN LEU GLN THR ILE THR LEU THR LYS THR HIS ILE ASP SEQRES 2 A 166 LEU TYR TYR MET LEU VAL GLN MET THR ASP GLU PHE TYR SEQRES 3 A 166 PRO GLN LEU SER ALA HIS GLY LYS GLN ALA VAL ILE HIS SEQRES 4 A 166 ALA PRO GLU ASP LEU THR VAL SER GLY ASP PRO ASP LYS SEQRES 5 A 166 LEU ALA ARG VAL PHE ASN ASN ILE LEU LYS ASN ALA ALA SEQRES 6 A 166 ALA TYR SER GLU ASP ASN SER ILE ILE ASP ILE THR ALA SEQRES 7 A 166 GLY LEU SER GLY ASP VAL VAL SER ILE GLU PHE LYS ASN SEQRES 8 A 166 THR GLY SER ILE PRO LYS ASP LYS LEU ALA ALA ILE PHE SEQRES 9 A 166 GLU LYS PHE TYR ARG LEU ASP ASN ALA ARG SER SER ASP SEQRES 10 A 166 THR GLY GLY ALA GLY LEU GLY LEU ALA ILE ALA LYS GLU SEQRES 11 A 166 ILE ILE VAL GLN HIS GLY GLY GLN ILE TYR ALA GLU SER SEQRES 12 A 166 ASN ASP ASN TYR THR THR PHE ARG VAL GLU LEU PRO ALA SEQRES 13 A 166 MET PRO ASP LEU VAL ASP LYS ARG ARG SER HET CD A 401 1 HET CD A 402 1 HETNAM CD CADMIUM ION FORMUL 2 CD 2(CD 2+) FORMUL 4 HOH *24(H2 O) HELIX 1 AA1 LEU A 232 ALA A 249 1 18 HELIX 2 AA2 ASP A 267 SER A 286 1 20 HELIX 3 AA3 PRO A 314 ALA A 319 1 6 HELIX 4 AA4 LEU A 343 HIS A 353 1 11 SHEET 1 AA1 2 ILE A 230 ASP A 231 0 SHEET 2 AA1 2 THR A 263 VAL A 264 -1 O VAL A 264 N ILE A 230 SHEET 1 AA2 5 GLN A 253 HIS A 257 0 SHEET 2 AA2 5 ILE A 291 SER A 299 1 O ILE A 292 N GLN A 253 SHEET 3 AA2 5 VAL A 302 THR A 310 -1 O GLU A 306 N THR A 295 SHEET 4 AA2 5 TYR A 365 PRO A 373 -1 O PHE A 368 N PHE A 307 SHEET 5 AA2 5 GLN A 356 SER A 361 -1 N TYR A 358 O ARG A 369 LINK NE2 HIS A 229 CD CD A 401 1555 1555 2.37 LINK OD1 ASP A 231 CD CD A 401 1555 1555 2.26 LINK OD2 ASP A 231 CD CD A 401 1555 1555 2.42 LINK ND1 HIS A 250 CD CD A 401 1555 4456 2.30 LINK ND1 HIS A 257 CD CD A 402 1555 1555 2.23 LINK OD1 ASP A 267 CD CD A 402 1555 1554 2.33 LINK OD2 ASP A 267 CD CD A 402 1555 1554 2.30 LINK OD1 ASP A 269 CD CD A 402 1555 1554 2.27 LINK OD2 ASP A 269 CD CD A 402 1555 1554 2.41 LINK OD1 ASP A 288 CD CD A 401 1555 4456 2.35 LINK OD2 ASP A 288 CD CD A 401 1555 4456 2.44 LINK CD CD A 402 O HOH A 521 1555 1556 2.61 CRYST1 69.830 94.400 29.770 90.00 90.00 90.00 P 21 21 2 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 0.014320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033591 0.00000