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Yorodumi- PDB-7v2b: Crystal Structure of VpsR display novel dimeric architecture and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v2b | ||||||
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Title | Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding. | ||||||
Components | VpsR | ||||||
Keywords | TRANSCRIPTION / X-ray crystallography / Biofilm / Fluorescence quenching / ATPase activity / second-messenger | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Chakrabortty, T. / Sen, U. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding. Authors: Chakrabortty, T. / Roy Chowdhury, S. / Ghosh, B. / Sen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v2b.cif.gz | 319.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v2b.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v2b_validation.pdf.gz | 953.1 KB | Display | wwPDB validaton report |
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Full document | 7v2b_full_validation.pdf.gz | 979.6 KB | Display | |
Data in XML | 7v2b_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 7v2b_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/7v2b ftp://data.pdbj.org/pub/pdb/validation_reports/v2/7v2b | HTTPS FTP |
-Related structure data
Related structure data | 7v2vC 7v3wC 7v4eC 1ny5S 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: 44722.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: vpsR / Plasmid: pet28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AQ41 #2: Chemical | 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: 3.55 Å3/Da / Density % sol: 61.45 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: AMS(0.8M) Bicene pH 8.8 / PH range: 8-8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→47.34 Å / Num. obs: 65219 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.812 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.057 / Rrim(I) all: 0.105 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2062 / CC1/2: 0.329 / Rpim(I) all: 1.002 / Rrim(I) all: 1.851 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NY5 Resolution: 3.2→47.273 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 32.39 / Stereochemistry target values: ML Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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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: 3.2→47.273 Å
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Refine LS restraints |
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LS refinement shell |
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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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