+Open data
-Basic information
Entry | Database: PDB / ID: 7ve6 | |||||||||
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Title | N-terminal domain of VraR | |||||||||
Components | Response regulator protein VraR | |||||||||
Keywords | DNA BINDING PROTEIN / two-component system | |||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / response to antibiotic / regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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 | 7ve6.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ve6.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ve6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/7ve6 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7ve6 | HTTPS FTP |
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-Related structure data
Related structure data | 7ve4C 7ve5C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 137 / Label seq-ID: 2 - 137
NCS oper: (Code: givenMatrix: (0.614316305434, 0.497461112397, -0.612493198763), (0.49016433004, -0.848882677402, -0.197831063191), (-0.618348127218, -0.178691470586, -0.765320163008)Vector: -40. ...NCS oper: (Code: given Matrix: (0.614316305434, 0.497461112397, -0.612493198763), Vector: |
-Components
#1: Protein | Mass: 23591.340 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria) Strain: Mu50 / ATCC 700699 / Gene: vraR, SAV1884 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A2Q1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.11 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-Hcl pH 8.0, 18% PEG 550MME (w/v), 5% Glycerol, 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: 0.9984 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9984 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→22.93 Å / Num. obs: 14756 / % possible obs: 97.24 % / Redundancy: 9.2 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 37.16 |
Reflection shell | Resolution: 2.77→2.87 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.142 / Num. unique obs: 1152 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IF4 Resolution: 2.77→22.93 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.56 / 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: 168.62 Å2 / Biso mean: 46.2841 Å2 / Biso min: 17.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.77→22.93 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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