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- PDB-6y1y: CheA dimerization domain of Treponema denticola -

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Basic information

Entry
Database: PDB / ID: 6y1y
TitleCheA dimerization domain of Treponema denticola
ComponentsCheA
KeywordsSIGNALING PROTEIN / Histidine kinase / dimerization domain / coiled-coil
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / ATP binding / cytoplasm
Histidine kinase domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / HPT domain superfamily / CheW-like domain / Histidine kinase/HSP90-like ATPase / Histidine kinase CheA-like, homodimeric domain / Signal transduction histidine kinase-related protein, C-terminal / CheW-like domain superfamily ...Histidine kinase domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / HPT domain superfamily / CheW-like domain / Histidine kinase/HSP90-like ATPase / Histidine kinase CheA-like, homodimeric domain / Signal transduction histidine kinase-related protein, C-terminal / CheW-like domain superfamily / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / Chemotaxis protein CheA, P2 response regulator-binding
Chemotaxis protein CheA
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsMuok, A.R. / Briegel, A. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122535 United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CheA
B: CheA


Theoretical massNumber of molelcules
Total (without water)29,5962
Polymers29,5962
Non-polymers00
Water5,693316
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-66 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.636, 28.770, 82.982
Angle α, β, γ (deg.)90.00, 114.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CheA /


Mass: 14797.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: cheA / Production host: Escherichia coli (E. coli) / References: UniProt: O85747
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.86 Å3/Da / Density % sol: 33.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Imidazole pH 7.0, 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→75.36 Å / Num. obs: 35178 / % possible obs: 96.72 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.041 / Rrim(I) all: 0.075 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 3490 / CC1/2: 0.94 / Rpim(I) all: 0.193 / Rrim(I) all: 0.35 / % possible all: 99.31

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
Cootmodel building
AMPLEphasing
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→75 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2112 1314 3.74 %
Rwork0.1873 --
Obs0.1882 35174 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 316 2344
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062052
X-RAY DIFFRACTIONf_angle_d0.9312757
X-RAY DIFFRACTIONf_dihedral_angle_d4.2261275
X-RAY DIFFRACTIONf_chiral_restr0.07318
X-RAY DIFFRACTIONf_plane_restr0.007351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.5-1.56010.23881430.21873705X-RAY DIFFRACTION99
1.5601-1.63110.26941460.20133759X-RAY DIFFRACTION100
1.6311-1.71710.23191460.19933740X-RAY DIFFRACTION99
1.7171-1.82470.2391440.20423738X-RAY DIFFRACTION99
1.8247-1.96560.23861460.19413750X-RAY DIFFRACTION100
1.9656-2.16340.21851450.17383734X-RAY DIFFRACTION99
2.1634-2.47640.17961460.17623758X-RAY DIFFRACTION99
2.4764-3.12010.21561480.18643805X-RAY DIFFRACTION99
3.1201-750.19231500.18473871X-RAY DIFFRACTION98

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