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- PDB-3hzh: Crystal structure of the CheX-CheY-BeF3-Mg+2 complex from Borreli... -

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Basic information

Entry
Database: PDB / ID: 3hzh
TitleCrystal structure of the CheX-CheY-BeF3-Mg+2 complex from Borrelia burgdorferi
Components
  • Chemotaxis operon protein (CheX)
  • Chemotaxis response regulator (CheY-3)
KeywordsSIGNALING PROTEIN / Chemotaxis / Phosphatase / Complex / Response Regulator / Receiver Domain / Two-Component Signal Transduction
Function / homology
Function and homology information


phosphorelay signal transduction system / chemotaxis / metal ion binding / identical protein binding
Similarity search - Function
CheC-like family / CheY-P phosphatase CheX-like / Chemotaxis phosphatase CheX-like domain / Chemotaxis phosphatase CheX / CheC-like / Chemotaxis protein chec / CheC-like superfamily / : / Response regulator receiver domain / cheY-homologous receiver domain ...CheC-like family / CheY-P phosphatase CheX-like / Chemotaxis phosphatase CheX-like domain / Chemotaxis phosphatase CheX / CheC-like / Chemotaxis protein chec / CheC-like superfamily / : / 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
CheC-like family protein / CheY
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsPazy, Y. / Silversmith, R.E. / Guarinari, M. / Zhao, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate.
Authors: Pazy, Y. / Motaleb, M.A. / Guarnieri, M.T. / Charon, N.W. / Zhao, R. / Silversmith, R.E.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis response regulator (CheY-3)
B: Chemotaxis operon protein (CheX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7993
Polymers36,7742
Non-polymers241
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-19 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.705, 63.705, 175.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chemotaxis response regulator (CheY-3)


Mass: 17589.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0672, CheY3 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/pREP4 / References: UniProt: O51615
#2: Protein Chemotaxis operon protein (CheX)


Mass: 19184.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0671, CheX / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/pREP4 / References: UniProt: O51614
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium Sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.96→29.64 Å / Num. all: 48321 / Num. obs: 45929 / % possible obs: 93.6 % / Redundancy: 6 % / Rsym value: 0.064 / Net I/σ(I): 26
Reflection shellResolution: 1.96→1.98 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.531 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
RESOLVEShelxDmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEShelxDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→29.64 Å
RfactorNum. reflection
Rfree0.259 -
Rwork0.248 -
all-48321
obs-45929
Displacement parametersBiso mean: 40.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.252 Å2-2.059 Å20 Å2
2---1.252 Å20 Å2
3---2.505 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 1 158 2389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg2.021
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

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