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- PDB-1bdj: COMPLEX STRUCTURE OF HPT DOMAIN AND CHEY -

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Basic information

Entry
Database: PDB / ID: 1bdj
TitleCOMPLEX STRUCTURE OF HPT DOMAIN AND CHEY
Components
  • AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB
  • CHEY
KeywordsCOMPLEX (CHEMOTAXIS/TRANSFERASE) / TWO-COMPONENT SYSTEM / HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN / ARCB / RESPONSE REGULATOR / CHEY / COMPLEX (CHEMOTAXIS-TRANSFERASE) / COMPLEX (CHEMOTAXIS-TRANSFERASE) complex
Function / homology
Function and homology information


peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / response to oxygen levels / internal peptidyl-lysine acetylation / thermotaxis ...peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / response to oxygen levels / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / chemotaxis / protein autophosphorylation / regulation of DNA-templated transcription / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily ...Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / : / Histidine kinase/HSP90-like ATPase / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheY / Aerobic respiration control sensor protein ArcB / Aerobic respiration control sensor protein ArcB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor protein ArcB complexed with the chemotaxis response regulator CheY.
Authors: Kato, M. / Shimizu, T. / Mizuno, T. / Hakoshima, T.
History
DepositionMay 10, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEY
B: AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0913
Polymers27,9952
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.175, 76.170, 83.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHEY / CHEMOTAXIS PROTEIN CHEY


Mass: 13981.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE RESPONSE REGULATOR / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-CHEY / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): BL21 / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Protein AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB


Mass: 14013.939 Da / Num. of mol.: 1
Fragment: HPT DOMAIN, THE HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSU2DH / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): DZ225
References: UniProt: P22763, UniProt: P0AEC3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 60 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Kato, M., (1998) Acta Crystallogr., D54, 140.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %PEG40001reservoir
2200 mMammonium sulfate1reservoir
312 %PEG40001drop
480 mMammonium sulfate1drop
512.8 mg/mlprotain1drop
620 mM1dropNaCl
710 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Nov 1, 1996 / Details: COLLIMATER
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.68 Å / Num. obs: 9392 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 46.3
Reflection shellResolution: 2.68→3.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 84.2
Reflection
*PLUS
Num. measured all: 40201
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.405

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
WEISdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0B (HPT DOMAIN) AND 1CHN (CHEY)

1a0b

1chn


Resolution: 2.68→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 488 5.3 %RANDOM
Rwork0.183 ---
obs0.183 9146 90.6 %-
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.68→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 5 44 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.61.5
X-RAY DIFFRACTIONx_mcangle_it2.652
X-RAY DIFFRACTIONx_scbond_it2.722
X-RAY DIFFRACTIONx_scangle_it4.412.5
LS refinement shellResolution: 2.68→2.8 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.388 40 4.5 %
Rwork0.312 842 -
obs--71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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