HEADER COMPLEX (CHEMOTAXIS/TRANSFERASE) 10-MAY-98 1BDJ TITLE COMPLEX STRUCTURE OF HPT DOMAIN AND CHEY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHEMOTAXIS PROTEIN CHEY; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE RESPONSE REGULATOR; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: HPT DOMAIN, THE HISTIDINE-CONTAINING PHOSPHOTRANSFER COMPND 11 DOMAIN; COMPND 12 EC: 2.7.3.-; COMPND 13 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: BL21; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7-CHEY; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 16 EXPRESSION_SYSTEM_VARIANT: DZ225; SOURCE 17 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PSU2DH KEYWDS TWO-COMPONENT SYSTEM, HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) KEYWDS 2 DOMAIN, ARCB, RESPONSE REGULATOR, CHEY, COMPLEX (CHEMOTAXIS- KEYWDS 3 TRANSFERASE), COMPLEX (CHEMOTAXIS-TRANSFERASE) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,T.MIZUNO,T.SHIMIZU,T.HAKOSHIMA REVDAT 6 22-MAY-24 1BDJ 1 REMARK REVDAT 5 02-AUG-23 1BDJ 1 REMARK REVDAT 4 29-NOV-17 1BDJ 1 HELIX REVDAT 3 18-SEP-13 1BDJ 1 REMARK VERSN REVDAT 2 24-FEB-09 1BDJ 1 VERSN REVDAT 1 11-MAY-99 1BDJ 0 JRNL AUTH M.KATO,T.SHIMIZU,T.MIZUNO,T.HAKOSHIMA JRNL TITL STRUCTURE OF THE HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) JRNL TITL 2 DOMAIN OF THE ANAEROBIC SENSOR PROTEIN ARCB COMPLEXED WITH JRNL TITL 3 THE CHEMOTAXIS RESPONSE REGULATOR CHEY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1257 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10393292 JRNL DOI 10.1107/S0907444999005053 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 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) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 9146 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) : 0.183 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 488 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 842 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 40 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1898 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.49 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.99 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 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) : 1.600 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.410 ; 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 : SO4.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : SO4.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1BDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B 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 : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATER REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 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 (%) : 92.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PDB ENTRY 1A0B (HPT DOMAIN) AND 1CHN (CHEY) REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING THE WEISSENBERG METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 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 27.58750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.63500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.63500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.58750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.08500 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B 652 REMARK 465 THR B 653 REMARK 465 GLU B 654 REMARK 465 GLU B 655 REMARK 465 ASN B 656 REMARK 465 SER B 657 REMARK 465 LYS B 775 REMARK 465 LYS B 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 ASP A 13 -98.63 -55.36 REMARK 500 SER A 15 -168.28 -125.82 REMARK 500 VAL A 40 -70.95 -60.47 REMARK 500 ASN A 62 -43.60 79.20 REMARK 500 MET A 63 116.94 -165.57 REMARK 500 MET A 78 36.06 -146.20 REMARK 500 GLU A 89 108.49 -58.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: PHD REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PHOSPHO-DONOR RESIDUE. REMARK 800 REMARK 800 SITE_IDENTIFIER: PHA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PHOSPHO-ACCEPTOR RESIDUE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 400 DBREF 1BDJ A 2 129 UNP P06143 CHEY_ECOLI 1 128 DBREF 1BDJ B 652 776 UNP P22763 ARCB_ECOLI 652 776 SEQRES 1 A 128 ALA ASP LYS GLU LEU LYS PHE LEU VAL VAL ASP ASP PHE SEQRES 2 A 128 SER THR MET ARG ARG ILE VAL ARG ASN LEU LEU LYS GLU SEQRES 3 A 128 LEU GLY PHE ASN ASN VAL GLU GLU ALA GLU ASP GLY VAL SEQRES 4 A 128 ASP ALA LEU ASN LYS LEU GLN ALA GLY GLY TYR GLY PHE SEQRES 5 A 128 VAL ILE SER ASP TRP ASN MET PRO ASN MET ASP GLY LEU SEQRES 6 A 128 GLU LEU LEU LYS THR ILE ARG ALA ASP GLY ALA MET SER SEQRES 7 A 128 ALA LEU PRO VAL LEU MET VAL THR ALA GLU ALA LYS LYS SEQRES 8 A 128 GLU ASN ILE ILE ALA ALA ALA GLN ALA GLY ALA SER GLY SEQRES 9 A 128 TYR VAL VAL LYS PRO PHE THR ALA ALA THR LEU GLU GLU SEQRES 10 A 128 LYS LEU ASN LYS ILE PHE GLU LYS LEU GLY MET SEQRES 1 B 125 THR THR GLU GLU ASN SER LYS SER GLU ALA LEU LEU ASP SEQRES 2 B 125 ILE PRO MET LEU GLU GLN TYR LEU GLU LEU VAL GLY PRO SEQRES 3 B 125 LYS LEU ILE THR ASP GLY LEU ALA VAL PHE GLU LYS MET SEQRES 4 B 125 MET PRO GLY TYR VAL SER VAL LEU GLU SER ASN LEU THR SEQRES 5 B 125 ALA GLN ASP LYS LYS GLY ILE VAL GLU GLU GLY HIS LYS SEQRES 6 B 125 ILE LYS GLY ALA ALA GLY SER VAL GLY LEU ARG HIS LEU SEQRES 7 B 125 GLN GLN LEU GLY GLN GLN ILE GLN SER PRO ASP LEU PRO SEQRES 8 B 125 ALA TRP GLU ASP ASN VAL GLY GLU TRP ILE GLU GLU MET SEQRES 9 B 125 LYS GLU GLU TRP ARG HIS ASP VAL GLU VAL LEU LYS ALA SEQRES 10 B 125 TRP VAL ALA LYS ALA THR LYS LYS HET SO4 A 400 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *44(H2 O) HELIX 1 H1 MET A 17 GLU A 27 1 11 HELIX 2 H2 GLY A 39 GLN A 47 1 9 HELIX 3 H3 GLY A 65 ALA A 74 1 10 HELIX 4 H4 LYS A 92 ALA A 101 1 10 HELIX 5 H5 ALA A 113 LEU A 127 1 15 HELIX 6 G1 GLY A 76 MET A 78 5 3 HELIX 7 A SER B 659 LEU B 662 1 4 HELIX 8 B ILE B 665 LEU B 674 1 10 HELIX 9 C LYS B 678 ALA B 704 1 27 HELIX 10 D LYS B 707 SER B 723 1 17 HELIX 11 E ARG B 727 ILE B 736 1 10 HELIX 12 F TRP B 744 ALA B 773 1 30 SHEET 1 A 5 LYS A 7 VAL A 11 0 SHEET 2 A 5 VAL A 33 ALA A 36 1 SHEET 3 A 5 TYR A 51 SER A 56 1 SHEET 4 A 5 VAL A 83 THR A 87 1 SHEET 5 A 5 GLY A 105 VAL A 108 1 CISPEP 1 LYS A 109 PRO A 110 0 0.07 SITE 1 PHD 1 HIS B 715 SITE 1 PHA 1 ASP A 57 SITE 1 AC1 6 ASP A 57 TRP A 58 ASN A 59 THR A 87 SITE 2 AC1 6 ALA A 88 LYS A 109 CRYST1 55.175 76.170 83.270 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 0.018124 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012009 0.00000