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- PDB-2ch4: Complex between Bacterial Chemotaxis histidine kinase CheA domain... -

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Basic information

Entry
Database: PDB / ID: 2ch4
TitleComplex between Bacterial Chemotaxis histidine kinase CheA domains P4 and P5 and receptor-adaptor protein CheW
Components
  • CHEMOTAXIS PROTEIN CHEA
  • CHEMOTAXIS PROTEIN CHEW
KeywordsTRANSFERASE/CHEMOTAXIS / CHEMOTAXIS / PROTEIN-PROTEIN COMPLEX / SIGNAL TRANSDUCTION / HISTIDINE KINASE / SENSORY TRANSDUCTION / PHOSPHORYLATION / TRANSFERASE / TRANSFERASE-CHEMOTAXIS complex
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / chemotaxis / protein domain specific binding / signal transduction / ATP binding / cytosol / cytoplasm
Similarity search - Function
CheA-289, Domain 4 / Chemotaxis protein CheW / Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain ...CheA-289, Domain 4 / Chemotaxis protein CheW / Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / SH3 Domains / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chemotaxis protein CheA / Chemotaxis protein CheW
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPark, S.Y. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Reconstruction of the Chemotaxis Receptor-Kinase Assembly
Authors: Park, S.Y. / Borbat, P.P. / Gonzalez-Bonet, G. / Bhatnagar, J. / Pollard, A.M. / Freed, J.H. / Bilwes, A.M. / Crane, B.R.
History
DepositionMar 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEMOTAXIS PROTEIN CHEA
B: CHEMOTAXIS PROTEIN CHEA
W: CHEMOTAXIS PROTEIN CHEW
Y: CHEMOTAXIS PROTEIN CHEW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0706
Polymers105,0584
Non-polymers1,0122
Water23413
1
A: CHEMOTAXIS PROTEIN CHEA
W: CHEMOTAXIS PROTEIN CHEW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0353
Polymers52,5292
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CHEMOTAXIS PROTEIN CHEA
Y: CHEMOTAXIS PROTEIN CHEW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0353
Polymers52,5292
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.600, 136.600, 231.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CHEMOTAXIS PROTEIN CHEA


Mass: 35551.121 Da / Num. of mol.: 2
Fragment: CHEA KINASE AND REGULATORY DOMAINS, RESIDUES 355-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Protein CHEMOTAXIS PROTEIN CHEW


Mass: 16977.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56311
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsK352G, I353S, R354H MUTATIONS INTRODUCED BY VECTOR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 76 %
Crystal growDetails: PEG 4K 3-5%,NA ACETATE 0.1M PH 4.5,ADPNP 1MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 27869 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 40
Reflection shellResolution: 3.5→3.6 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 10 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1B3Q AND 1K0S

1b3q

1k0s


Resolution: 3.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE MOST RELEVANT BIOMOLECULE FOR THE CHEA DOMAINS P4-P5-CHEW COMPLEX IS PROBABLY MOL B (352- 672) - MOL Y. IN MOL A, THE ASSOCIATION BETWEEN DOMAINS P4 AND P5 IS PROBABLY AN ARTIFACT DUE TO ...Details: THE MOST RELEVANT BIOMOLECULE FOR THE CHEA DOMAINS P4-P5-CHEW COMPLEX IS PROBABLY MOL B (352- 672) - MOL Y. IN MOL A, THE ASSOCIATION BETWEEN DOMAINS P4 AND P5 IS PROBABLY AN ARTIFACT DUE TO THE USE OF A TRUNCATED CHEA FRAGMENT. CHEA DOMAIN P3 IN PDB ENTRY 1B3Q BINDS P5 WHERE P4 LIES IN MOLA OF THIS ENTRY. DISORDERED REGIONS WERE MODELLED IN POLYGLY OR POLYALA OR OMITTED IN MOL B (B493-B506 MISSING). DOMAIN CHEA-P4 (MOL B RESIDUES 352-540), WHICH IS IN CONTACT WITH A LARGE SOLVENT CHANNEL IS INCREASINGLY DISORDERED AS IT NEARS THE CHANNEL REGION, RESULTING IN VERY HIGH B-FACTORS. REMOVING OR KEEPING THESE REGIONS IN THE REFINEMENT HAS NO IMPACT ON THE R-FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2783 10 %RANDOM
Rwork0.255 ---
obs0.255 27869 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.242 e/Å3
Displacement parametersBiso mean: 120 Å2
Baniso -1Baniso -2Baniso -3
1-5.093 Å20 Å20 Å2
2---3.912 Å20 Å2
3----1.1181 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 62 13 7130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.6 Å
RfactorNum. reflection% reflection
Rfree0.32 183 -
Rwork0.26 --
obs--100 %

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