[English] 日本語
Yorodumi- PDB-1mvo: Crystal structure of the PhoP receiver domain from Bacillus subtilis -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mvo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the PhoP receiver domain from Bacillus subtilis | ||||||
Components | PhoP response regulator | ||||||
Keywords | TRANSCRIPTION / PHOSPHATE REGULON / TRANSCRIPTIONAL REGULATORY PROTEIN / ALPHA/BETA DOUBLY WOUND FOLD / RESPONSE REGULATOR / PHOSPHORYLATION / ASYMMETRIC INTERFACE / TANDEM ASSOCIATION / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | Function and homology information phosphate ion transport / phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Birck, C. / Chen, Y. / Hulett, F.M. / Samama, J.P. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: J.BACTERIOL. / Year: 2003 Title: The Crystal Structure of the Phosphorylation Domain in PhoP Reveals a Functional Tandem Association Mediated by an Asymmetric Interface Authors: Birck, C. / Chen, Y. / Hulett, F.M. / Samama, J.P. #1: Journal: J.BACTERIOL. / Year: 2003 Title: Residue R113 Is Essential for PhoP Dimerization and Function: a Residue Buried in the Asymmetric PhoP Dimer Interface Determined in the PhoPN Three-Dimensional Crystal Structure Authors: Chen, Y. / Birck, C. / Samama, J.P. / Hulett, F.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mvo.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mvo.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mvo_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1mvo_full_validation.pdf.gz | 420.4 KB | Display | |
Data in XML | 1mvo_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1mvo_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/1mvo ftp://data.pdbj.org/pub/pdb/validation_reports/mv/1mvo | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation : x+1/2, -y+3/2, -z+3/4 |
-Components
#1: Protein | Mass: 15546.987 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PHOP / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13792 | ||
---|---|---|---|
#2: Chemical | ChemComp-MN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 10000, sodium citrate, PEG MME 550, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→27 Å / Num. all: 18122 / Num. obs: 18122 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2775 / Rsym value: 0.187 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 27.1 Å / Num. obs: 18249 / % possible obs: 92 % / Num. measured all: 224913 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Metal-free PhoPN structure solved by MAD Resolution: 1.6→27 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used weighted full matrix maximum likelihood procedure
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.523 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→27 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.66 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 27.1 Å / Num. reflection obs: 17225 / Rfactor Rfree: 0.233 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |