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- PDB-2f9z: Complex between the chemotaxis deamidase CheD and the chemotaxis ... -

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Basic information

Entry
Database: PDB / ID: 2f9z
TitleComplex between the chemotaxis deamidase CheD and the chemotaxis phosphatase CheC from Thermotoga maritima
Components
  • PROTEIN (chemotaxis methylation protein)
  • chemotaxis protein CheC
KeywordsSIGNALING PROTEIN / bacterial chemotaxis / signal transduction / receptor deamidase / aspartyl phosphatase / protein complex / reciprocal regulation
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / Hydrolases / chemotaxis / hydrolase activity
Similarity search - Function
60s Ribosomal Protein L30; Chain: A; - #200 / Chemoreceptor glutamine deamidase CheD / CheD-like superfamily / CheD chemotactic sensory transduction / : / CheC-like protein / CheC-like family / : / CheC-like / Cytotoxic necrotizing factor-like, catalytic ...60s Ribosomal Protein L30; Chain: A; - #200 / Chemoreceptor glutamine deamidase CheD / CheD-like superfamily / CheD chemotactic sensory transduction / : / CheC-like protein / CheC-like family / : / CheC-like / Cytotoxic necrotizing factor-like, catalytic / Chemotaxis protein chec / CheC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemoreceptor glutamine deamidase CheD / CheY-P phosphatase CheC
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChao, X. / Park, S.Y. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: A receptor-modifying deamidase in complex with a signaling phosphatase reveals reciprocal regulation.
Authors: Chao, X. / Muff, T.J. / Park, S.Y. / Zhang, S. / Pollard, A.M. / Ordal, G.W. / Bilwes, A.M. / Crane, B.R.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chemotaxis protein CheC
B: chemotaxis protein CheC
C: PROTEIN (chemotaxis methylation protein)
D: PROTEIN (chemotaxis methylation protein)


Theoretical massNumber of molelcules
Total (without water)78,9234
Polymers78,9234
Non-polymers00
Water7,062392
1
A: chemotaxis protein CheC
C: PROTEIN (chemotaxis methylation protein)


Theoretical massNumber of molelcules
Total (without water)39,4612
Polymers39,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-15 kcal/mol
Surface area15560 Å2
MethodPISA
2
B: chemotaxis protein CheC
D: PROTEIN (chemotaxis methylation protein)


Theoretical massNumber of molelcules
Total (without water)39,4612
Polymers39,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-12 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.080, 66.080, 161.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein chemotaxis protein CheC


Mass: 22567.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0904 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X006
#2: Protein PROTEIN (chemotaxis methylation protein)


Mass: 16893.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0903 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X005
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.1M Tris, 0.25M Lithium Sulfate, 0.1M Cesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 32861 / Num. obs: 32861 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.111
Reflection shellResolution: 2.4→2.48 Å / Rsym value: 0.306 / % possible all: 89.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XKR

1xkr


Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1630 -RANDOM
Rwork0.211 ---
all0.211 32961 --
obs0.211 32861 93.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.396 Å2-3.942 Å20 Å2
2--0.396 Å20 Å2
3----0.793 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 0 392 5552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7

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