HEADER HISTIDINE KINASE 27-NOV-97 1A0B TITLE HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM TITLE 2 ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL HPT DOMAIN; COMPND 5 EC: 2.7.3.-; COMPND 6 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_STRAIN: K-12; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DZ225; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSU2DH KEYWDS HISTIDINE KINASE, PHOSPHOTRANSFER, TWO-COMPONENT SYSTEM, KEYWDS 2 FOUR-HELIX BUNDLE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,T.MIZUNO,T.SHIMIZU,T.HAKOSHIMA REVDAT 2 24-FEB-09 1A0B 1 VERSN REVDAT 1 18-MAR-98 1A0B 0 JRNL AUTH M.KATO,T.MIZUNO,T.SHIMIZU,T.HAKOSHIMA JRNL TITL INSIGHTS INTO MULTISTEP PHOSPHORELAY FROM THE JRNL TITL 2 CRYSTAL STRUCTURE OF THE C-TERMINAL HPT DOMAIN OF JRNL TITL 3 ARCB. JRNL REF CELL(CAMBRIDGE,MASS.) V. 88 717 1997 JRNL REFN ISSN 0092-8674 JRNL PMID 9054511 JRNL DOI 10.1016/S0092-8674(00)81914-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.KATO,K.ISHIGE,T.MIZUNO,T.SHIMIZU,T.HAKOSHIMA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 A HISTIDINE KINASE DOMAIN OF THE ANAEROBIC SENSOR REMARK 1 TITL 3 PROTEIN ARCB FROM ESCHERICHIA COLI REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 1214 1996 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 6792 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 742 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 640 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 92 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.34 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) : 1.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.450 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.310 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A0B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 4.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6999 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1, XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 12.5% REMARK 280 PEGMME 550, 5 MM ZNSO4, 50 MM ACETIC ACID/SODIUM ACETATE REMARK 280 BUFFER, PH 4.1 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 15.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.46500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.46500 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 THR A 652 REMARK 465 THR A 653 REMARK 465 GLU A 654 REMARK 465 GLU A 655 REMARK 465 ASN A 656 REMARK 465 SER A 657 REMARK 465 LYS A 775 REMARK 465 LYS A 776 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 SER A 738 79.86 -111.01 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 810 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 824 DISTANCE = 7.21 ANGSTROMS REMARK 525 HOH A 849 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH A 861 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A 864 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 868 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH A 870 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH A 875 DISTANCE = 9.20 ANGSTROMS REMARK 525 HOH A 885 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH A 902 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A 913 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH A 919 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 920 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 921 DISTANCE = 6.69 ANGSTROMS 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 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 728 NE2 REMARK 620 2 GLU A 758 OE1 98.2 REMARK 620 3 GLU A 758 OE2 101.5 58.7 REMARK 620 4 GLU A 754 OE2 118.2 143.4 112.8 REMARK 620 5 ASP A 746 OD2 125.6 78.1 120.1 77.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN BINDING SITE. REMARK 800 SITE_IDENTIFIER: PHB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PHOSPHORYLATION SITE. REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 800 DBREF 1A0B A 652 776 UNP P22763 ARCB_ECOLI 652 776 SEQRES 1 A 125 THR THR GLU GLU ASN SER LYS SER GLU ALA LEU LEU ASP SEQRES 2 A 125 ILE PRO MET LEU GLU GLN TYR LEU GLU LEU VAL GLY PRO SEQRES 3 A 125 LYS LEU ILE THR ASP GLY LEU ALA VAL PHE GLU LYS MET SEQRES 4 A 125 MET PRO GLY TYR VAL SER VAL LEU GLU SER ASN LEU THR SEQRES 5 A 125 ALA GLN ASP LYS LYS GLY ILE VAL GLU GLU GLY HIS LYS SEQRES 6 A 125 ILE LYS GLY ALA ALA GLY SER VAL GLY LEU ARG HIS LEU SEQRES 7 A 125 GLN GLN LEU GLY GLN GLN ILE GLN SER PRO ASP LEU PRO SEQRES 8 A 125 ALA TRP GLU ASP ASN VAL GLY GLU TRP ILE GLU GLU MET SEQRES 9 A 125 LYS GLU GLU TRP ARG HIS ASP VAL GLU VAL LEU LYS ALA SEQRES 10 A 125 TRP VAL ALA LYS ALA THR LYS LYS HET ZN A 800 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *121(H2 O) HELIX 1 1 SER A 659 LEU A 662 1 4 HELIX 2 2 ILE A 665 LEU A 674 1 10 HELIX 3 3 PRO A 677 THR A 703 1 27 HELIX 4 4 LYS A 707 VAL A 724 1 18 HELIX 5 5 ARG A 727 ILE A 736 1 10 HELIX 6 6 TRP A 744 LYS A 772 1 29 LINK ZN ZN A 800 NE2 HIS A 728 1555 1555 2.09 LINK ZN ZN A 800 OE1 GLU A 758 1555 1555 2.40 LINK ZN ZN A 800 OE2 GLU A 758 1555 1555 2.07 LINK ZN ZN A 800 OE2 GLU A 754 1555 1555 2.46 LINK ZN ZN A 800 OD2 ASP A 746 1555 3746 2.33 SITE 1 ZNB 4 HIS A 728 ASP A 746 GLU A 754 GLU A 758 SITE 1 PHB 1 HIS A 715 SITE 1 AC1 4 HIS A 728 ASP A 746 GLU A 754 GLU A 758 CRYST1 30.560 34.930 110.780 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 0.032723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009027 0.00000 MASTER 295 0 1 6 0 0 3 6 0 0 0 10 END