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Yorodumi- PDB-7v4e: Crystal Structure of VpsR display novel dimeric architecture and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v4e | ||||||
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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: 4 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 | 7v4e.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v4e.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v4e_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7v4e_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7v4e_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 7v4e_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/7v4e ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v4e | HTTPS FTP |
-Related structure data
Related structure data | 7v2bC 7v2vC 7v3wC 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AQ41 #2: Chemical | #3: 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: 3.75 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8M AMS, Bicine pH 8.8, NaCl 300mM / 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: 0.974 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021 / Details: bent cylindrical |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.974 Å / Relative weight: 1 |
Reflection | Resolution: 4→48.162 Å / Num. obs: 19802 / % possible obs: 95 % / Redundancy: 3.3 % / CC1/2: 0.95 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.342 / Num. unique obs: 1095 / CC1/2: 0.86 / Rpim(I) all: 0.211 / Rrim(I) all: 0.405 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NY5 Resolution: 4→48.162 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 34.87 / 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: 4→48.162 Å
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Refine LS restraints |
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LS refinement shell |
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