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- PDB-3h1e: Crystal structure of Mg(2+) and BeH(3)(-)-bound CheY of Helicobac... -

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Basic information

Entry
Database: PDB / ID: 3h1e
TitleCrystal structure of Mg(2+) and BeH(3)(-)-bound CheY of Helicobacter pylori
ComponentsChemotaxis protein cheY homolog
KeywordsSIGNALING PROTEIN / chemotaxis / BeF3-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
BERYLLIUM TRIFLUORIDE ION / Chemotaxis protein CheY1
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 1.3Jun 4, 2025Group: Structure summary / Category: pdbx_entry_details

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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)14,5555
Polymers14,3451
Non-polymers2114
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.956, 38.098, 38.885
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

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Components

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


Mass: 14344.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: CheY1 / Plasmid: pGEX-6P-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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.778725 Å3/Da / Density % sol: 30.849339 %
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, 1:10 beryllium, 1:100 sodium fluoride, 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 21, 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→33.32 Å / Num. obs: 4888 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.27 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 55.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.36 % / Rmerge(I) obs: 0.029 / Mean I/σ(I) obs: 39 / % possible all: 91.8

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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: 2.4→33.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.156 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R Free: 0.291
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22013 167 4.4 %RANDOM
Rwork0.15137 ---
obs0.15449 3613 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.05 Å2
2--0.14 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 11 58 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022985
X-RAY DIFFRACTIONr_bond_other_d0.0020.02665
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9931330
X-RAY DIFFRACTIONr_angle_other_deg2.4331645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3925.64139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08515195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.323155
X-RAY DIFFRACTIONr_chiral_restr0.0670.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02168
X-RAY DIFFRACTIONr_mcbond_it0.4811.5611
X-RAY DIFFRACTIONr_mcbond_other0.0981.5248
X-RAY DIFFRACTIONr_mcangle_it0.9262996
X-RAY DIFFRACTIONr_scbond_it1.5433374
X-RAY DIFFRACTIONr_scangle_it2.5244.5334
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 6 -
Rwork0.177 223 -
obs--84.19 %

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