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- PDB-3h1f: Crystal structure of CheY mutant D53A of Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 3h1f
TitleCrystal structure of CheY mutant D53A of Helicobacter pylori
ComponentsChemotaxis protein cheY homolog
KeywordsSIGNALING PROTEIN / chemotaxis / sulfate-bound cheY / Cytoplasm / Flagellar rotation / Magnesium / Metal-binding / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY1
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLam, K.H. / Ling, T.K. / Au, S.W.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Crystal structure of activated CheY1 from Helicobacter pylori.
Authors: Lam, K.H. / Ling, T.K. / Au, S.W.
History
DepositionApr 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein cheY homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5174
Polymers14,3011
Non-polymers2163
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.335, 38.081, 38.639
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chemotaxis protein cheY homolog / Chemotaxis protein CheY1


Mass: 14300.582 Da / Num. of mol.: 1 / Mutation: D53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: CheY1 / Plasmid: pgex-6-2 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: P71403
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.778048 Å3/Da / Density % sol: 30.823023 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium acetate, 35% MPEG2000, 0.05M ammonium sulfate, 1mM Magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2007 / Details: mirrors
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→36.88 Å / Num. obs: 4993 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.78 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.5 / % possible all: 97

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.4.0077refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GWG

3gwg


Resolution: 2.2→15.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.138 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.244
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23256 230 4.6 %RANDOM
Rwork0.17986 ---
obs0.1824 4747 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.961 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20.54 Å2
2---0.73 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 11 63 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022983
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9951329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.17925.52638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.525155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021689
X-RAY DIFFRACTIONr_mcbond_it0.6451.5611
X-RAY DIFFRACTIONr_mcangle_it1.1882995
X-RAY DIFFRACTIONr_scbond_it2.3463372
X-RAY DIFFRACTIONr_scangle_it3.5044.5334
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 12 -
Rwork0.246 343 -
obs--95.95 %

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