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- PDB-3kyj: Crystal structure of the P1 domain of CheA3 in complex with CheY6... -

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Basic information

Entry
Database: PDB / ID: 3kyj
TitleCrystal structure of the P1 domain of CheA3 in complex with CheY6 from R. sphaeroides
Components
  • CheY6 protein
  • Putative histidine protein kinase
KeywordsTRANSFERASE / protein-protein interaction / histidine kinase / response regulator / phosphorylation / specificity / Kinase
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / phosphorelay signal transduction system / chemotaxis
Similarity search - Function
HPT domain / 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 ...HPT domain / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheA / CheY6 protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsBell, C.H. / Porter, S.L. / Armitage, J.P. / Stuart, D.I.
CitationJournal: Plos Biol. / Year: 2010
Title: Using structural information to change the phosphotransfer specificity of a two-component chemotaxis signalling complex
Authors: Bell, C.H. / Porter, S.L. / Strawson, A. / Stuart, D.I. / Armitage, J.P.
History
DepositionDec 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative histidine protein kinase
B: CheY6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2833
Polymers31,2602
Non-polymers231
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.718, 62.011, 48.911
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative histidine protein kinase / CheA3


Mass: 15539.404 Da / Num. of mol.: 1 / Fragment: UNP residues 2-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: WS8N / Gene: cheA3 / Plasmid: pQE60 / Production host: Escherichia Coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8KLS0
#2: Protein CheY6 protein


Mass: 15720.257 Da / Num. of mol.: 1 / Fragment: UNP residues 2-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: WS8N / Gene: cheY6 / Plasmid: pQE60 / Production host: Escherichia Coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8KLS1
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.08 Å3/Da / Density % sol: 40.87 % / Mosaicity: 0.149 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 9
Details: 100mM Bicine, pH 9, 1M LiCl, 20% (w/v) PEG 6000, vapor diffusion, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 68797 / % possible obs: 85.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.053 / Χ2: 1.053 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.2-1.242.10.48328911.15936.2
1.24-1.292.30.36943981.16455
1.29-1.352.60.24958571.16173.7
1.35-1.423.30.17975301.16594.4
1.42-1.514.50.16279701.05499.1
1.51-1.637.20.15379621.0399.6
1.63-1.797.20.09379670.99599.8
1.79-2.057.20.05580461.043100
2.05-2.5960.06480311.045100
2.59-506.20.04881451.072100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.4_129refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.4→37.942 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.17 / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2553 5.08 %
Rwork0.17 --
obs0.172 50287 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.636 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 142.11 Å2 / Biso mean: 29.814 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.561 Å2-0 Å2-2.886 Å2
2--4.829 Å2-0 Å2
3----3.268 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 1 273 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012069
X-RAY DIFFRACTIONf_angle_d1.222816
X-RAY DIFFRACTIONf_chiral_restr0.065334
X-RAY DIFFRACTIONf_plane_restr0.005366
X-RAY DIFFRACTIONf_dihedral_angle_d16.034812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4270.2281470.1752589273699
1.427-1.4560.2711420.1692633277599
1.456-1.4880.2131380.1572617275599
1.488-1.5220.1951420.1552642278499
1.522-1.560.1871430.1522617276099
1.56-1.6030.211530.14826262779100
1.603-1.650.1931410.14326402781100
1.65-1.7030.1991360.14326352771100
1.703-1.7640.191480.14326582806100
1.764-1.8340.1861290.14626852814100
1.834-1.9180.2331260.15226432769100
1.918-2.0190.181340.15626732807100
2.019-2.1460.1861520.15226652817100
2.146-2.3110.2171420.15126722814100
2.311-2.5440.1771460.15826532799100
2.544-2.9120.221400.1726822822100
2.912-3.6680.2051430.17526822825100
3.668-37.9560.21510.18427222873100

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