+Open data
-Basic information
Entry | Database: PDB / ID: 2zpm | ||||||
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Title | Crystal structure analysis of PDZ domain B | ||||||
Components | Regulator of sigma E protease | ||||||
Keywords | HYDROLASE / metalloproteinase / membrane protein / PDZ domain / Inner membrane / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zinc | ||||||
Function / homology | Function and homology information anti-sigma factor antagonist activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / cellular response to cell envelope stress / metalloendopeptidase activity / positive regulation of DNA-templated transcription / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å | ||||||
Authors | Inaba, K. / Suzuki, M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure analysis of PDZ-domain B Authors: Inaba, K. / Suzuki, M. / Maegawa, K. / Akiyama, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zpm.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpm.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zpm_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 2zpm_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 2zpm_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 2zpm_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpm ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9815.257 Da / Num. of mol.: 1 / Fragment: PDZ-domain B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pGEX-5X-1 / Production host: Escherichia coli (E. coli) References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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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: 1.9 Å3/Da / Density % sol: 35.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 25% PEG3350, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.65 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→21.47 Å / Num. obs: 42333 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 0.98→1.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.9 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.98→20.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.227 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→20.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.981→1.006 Å / Total num. of bins used: 20
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