+Open data
-Basic information
Entry | Database: PDB / ID: 6azr | ||||||
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Title | Crystal structure of the T264A HK853cp-BeF3-RR468 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Kinase / Phosphatase / Response Regulator / Two-Component System | ||||||
Function / homology | Function and homology information histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / nucleotide binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.628 Å | ||||||
Authors | Rose, J. / Zhou, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: A pH-gated conformational switch regulates the phosphatase activity of bifunctional HisKA-family histidine kinases. Authors: Liu, Y. / Rose, J. / Huang, S. / Hu, Y. / Wu, Q. / Wang, D. / Li, C. / Liu, M. / Zhou, P. / Jiang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6azr.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6azr.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 6azr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6azr ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azr | HTTPS FTP |
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-Related structure data
Related structure data | 5uhtC 3dgeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29479.449 Da / Num. of mol.: 2 / Fragment: UNP residues 232-489 / Mutation: T264A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0853 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV7 #2: Protein | Mass: 14044.450 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_0465 / Production host: Escherichia coli (E. coli) / References: UniProt: R4NNQ5, UniProt: Q9WYT9*PLUS #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.42 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.05 M citric acid , 0.104 M ammonium sulfate, 2 mM AMPPNP, 5 mM Tris, 3.5 mM MgCl2, 2.5 mM BeCl2, 15 mM NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.628→45.5 Å / Num. obs: 13230 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1444 / Rrim(I) all: 0.1647 / Net I/σ(I): 6.56 |
Reflection shell | Resolution: 3.628→3.758 Å / Redundancy: 4 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.41 / Num. unique all: 1272 / CC1/2: 0.767 / Rrim(I) all: 0.6143 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DGE Resolution: 3.628→45.497 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.628→45.497 Å
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Refine LS restraints |
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LS refinement shell |
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