+Open data
-Basic information
Entry | Database: PDB / ID: 7ve4 | |||||||||
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Title | C-terminal domain of VraR | |||||||||
Components | DNA-binding response regulator | |||||||||
Keywords | DNA BINDING PROTEIN / two-component system | |||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||
Authors | Kumar, J.V. / Chen, C. / Hsu, C.H. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Structural insights into DNA binding domain of vancomycin-resistance-associated response regulator in complex with its promoter DNA from Staphylococcus aureus. Authors: Kumar, J.V. / Tseng, T.S. / Lou, Y.C. / Wei, S.Y. / Wu, T.H. / Tang, H.C. / Chiu, Y.C. / Hsu, C.H. / Chen, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ve4.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ve4.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ve4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/7ve4 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7ve4 | HTTPS FTP |
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-Related structure data
Related structure data | 7ve5C 7ve6C 4if4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8342.708 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: BSZ10_05280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q8DEZ3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 69.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-Hcl pH 8.5, 16% PEG 4000 (w/v), 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jan 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→24.31 Å / Num. obs: 9739 / % possible obs: 98.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.25 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.88 |
Reflection shell | Resolution: 1.87→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Num. unique obs: 842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IF4 Resolution: 1.87→24.309 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.99 Å2 / Biso mean: 25.2262 Å2 / Biso min: 7.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→24.309 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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