HEADER TRANSFERASE 02-APR-01 1ID0 TITLE CRYSTAL STRUCTURE OF THE NUCLEOTIDE BOND CONFORMATION OF PHOQ KINASE TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOQ HISTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: SENSOR PROTEIN PHOQ; COMPND 6 EC: 2.7.1.37; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PAE4D; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PAED4QKD KEYWDS HISTIDINE KINASE, PHOQ/PHOP, SIGNAL TRANSDUCTION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MARINA,C.MOTT,A.AUYZENBERG,C.D.WALDBURGER,W.A.HENDRICKSON REVDAT 6 07-FEB-24 1ID0 1 REMARK LINK REVDAT 5 01-FEB-17 1ID0 1 AUTHOR VERSN REVDAT 4 24-FEB-09 1ID0 1 VERSN REVDAT 3 01-APR-03 1ID0 1 JRNL REVDAT 2 28-DEC-01 1ID0 1 JRNL REVDAT 1 17-OCT-01 1ID0 0 JRNL AUTH A.MARINA,C.MOTT,A.AUYZENBERG,W.A.HENDRICKSON,C.D.WALDBURGER JRNL TITL STRUCTURAL AND MUTATIONAL ANALYSIS OF THE PHOQ HISTIDINE JRNL TITL 2 KINASE CATALYTIC DOMAIN. INSIGHT INTO THE REACTION JRNL TITL 3 MECHANISM. JRNL REF J.BIOL.CHEM. V. 276 41182 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11493605 JRNL DOI 10.1074/JBC.M106080200 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 956397.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19159 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1400 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1156 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 90 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1137 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.39000 REMARK 3 B22 (A**2) : -1.57000 REMARK 3 B33 (A**2) : 4.96000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 5.200 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 46.29 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ANP_MUTL.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ANP_MUTL.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ID0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013170. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 22.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18600 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: MAD REMARK 200 SOFTWARE USED: MADSYS, MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A CACODYLATE, PEG 1500, MG ACETATE, PH REMARK 280 6.5, VAPORDIFFUSION, HANGING DROP, TEMPERATURE 277K, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 21.75150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.88200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.50200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.88200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.75150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.50200 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 SER A 481 REMARK 465 ALA A 482 REMARK 465 PRO A 483 REMARK 465 LYS A 484 REMARK 465 ASP A 485 REMARK 465 GLU A 486 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 376 O HOH A 189 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 396 -38.84 -151.16 REMARK 500 THR A 405 -165.43 -118.25 REMARK 500 ARG A 434 56.54 -93.73 REMARK 500 ASP A 436 68.40 26.61 REMARK 500 LEU A 438 68.38 -68.19 REMARK 500 PRO A 440 -11.03 -48.62 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 700 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 84 O REMARK 620 2 ASN A 385 OD1 78.9 REMARK 620 3 GLN A 442 OE1 90.7 107.9 REMARK 620 4 ANP A 487 O2G 86.4 153.7 93.9 REMARK 620 5 ANP A 487 O2B 161.4 119.3 79.9 78.3 REMARK 620 6 ANP A 487 O2A 109.6 91.4 154.5 73.0 76.1 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 MG A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 487 DBREF 1ID0 A 335 486 UNP P23837 PHOQ_ECOLI 335 486 SEQRES 1 A 152 ARG GLU LEU HIS PRO VAL ALA PRO LEU LEU ASP ASN LEU SEQRES 2 A 152 THR SER ALA LEU ASN LYS VAL TYR GLN ARG LYS GLY VAL SEQRES 3 A 152 ASN ILE SER LEU ASP ILE SER PRO GLU ILE SER PHE VAL SEQRES 4 A 152 GLY GLU GLN ASN ASP PHE VAL GLU VAL MET GLY ASN VAL SEQRES 5 A 152 LEU ASP ASN ALA CYS LYS TYR CYS LEU GLU PHE VAL GLU SEQRES 6 A 152 ILE SER ALA ARG GLN THR ASP GLU HIS LEU TYR ILE VAL SEQRES 7 A 152 VAL GLU ASP ASP GLY PRO GLY ILE PRO LEU SER LYS ARG SEQRES 8 A 152 GLU VAL ILE PHE ASP ARG GLY GLN ARG VAL ASP THR LEU SEQRES 9 A 152 ARG PRO GLY GLN GLY VAL GLY LEU ALA VAL ALA ARG GLU SEQRES 10 A 152 ILE THR GLU GLN TYR GLU GLY LYS ILE VAL ALA GLY GLU SEQRES 11 A 152 SER MET LEU GLY GLY ALA ARG MET GLU VAL ILE PHE GLY SEQRES 12 A 152 ARG GLN HIS SER ALA PRO LYS ASP GLU HET MG A 700 1 HET ANP A 487 31 HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 2 MG MG 2+ FORMUL 3 ANP C10 H17 N6 O12 P3 FORMUL 4 HOH *189(H2 O) HELIX 1 1 VAL A 340 TYR A 355 1 16 HELIX 2 2 GLU A 375 CYS A 394 1 20 HELIX 3 3 PRO A 421 ARG A 425 5 5 HELIX 4 4 GLU A 426 ASP A 430 5 5 HELIX 5 5 GLY A 445 TYR A 456 1 12 SHEET 1 A 2 LEU A 337 PRO A 339 0 SHEET 2 A 2 SER A 371 VAL A 373 -1 O PHE A 372 N HIS A 338 SHEET 1 B 5 ASN A 361 ASP A 365 0 SHEET 2 B 5 PHE A 397 GLN A 404 1 N VAL A 398 O ASN A 361 SHEET 3 B 5 LEU A 409 ASP A 415 -1 N TYR A 410 O ARG A 403 SHEET 4 B 5 ALA A 470 PHE A 476 -1 O ALA A 470 N ASP A 415 SHEET 5 B 5 LYS A 459 GLU A 464 -1 O LYS A 459 N ILE A 475 LINK O HOH A 84 MG MG A 700 1555 1555 2.28 LINK OD1 ASN A 385 MG MG A 700 1555 1555 2.31 LINK OE1 GLN A 442 MG MG A 700 1555 1555 2.49 LINK O2G ANP A 487 MG MG A 700 1555 1555 2.51 LINK O2B ANP A 487 MG MG A 700 1555 1555 2.43 LINK O2A ANP A 487 MG MG A 700 1555 1555 2.76 SITE 1 AC1 4 HOH A 84 ASN A 385 GLN A 442 ANP A 487 SITE 1 AC2 20 HOH A 5 HOH A 16 HOH A 67 HOH A 126 SITE 2 AC2 20 HOH A 184 ASN A 385 ASN A 389 LYS A 392 SITE 3 AC2 20 TYR A 393 ASP A 415 GLY A 419 ILE A 420 SITE 4 AC2 20 ILE A 428 ARG A 434 ARG A 439 GLN A 442 SITE 5 AC2 20 GLY A 445 LEU A 446 ALA A 470 MG A 700 CRYST1 43.503 45.004 71.764 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 0.022987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013935 0.00000