+Open data
-Basic information
Entry | Database: PDB / ID: 2zpl | ||||||
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Title | Crystal structure analysis of PDZ domain A | ||||||
Components | Regulator of sigma E protease | ||||||
Keywords | HYDROLASE / metalloproteinase / membrane protein / PDZ-domain / Inner membrane / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane | ||||||
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: 1.7 Å | ||||||
Authors | Inaba, K. / Suzuki, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure analysis of PDZ-domain A 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 | 2zpl.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpl.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zpl_validation.pdf.gz | 420.2 KB | Display | wwPDB validaton report |
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Full document | 2zpl_full_validation.pdf.gz | 423.2 KB | Display | |
Data in XML | 2zpl_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 2zpl_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpl ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10521.553 Da / Num. of mol.: 3 / Fragment: PDZ-domain A / Mutation: L169M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.07 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 17% PEG2000mme, 85mM Tris-HCl, 8.5mM NiCl2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→18.55 Å / Num. obs: 27607 / % possible obs: 99 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3842 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→18.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.199 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The structure factor data is twinned data. The twinning operator and fraction are (h, k, l, 0.642), (-h, h+k, -l, 0.019), (-h-k, k, -l, 0.319) and (-h, -k, l, 0.020).
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.943 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→18.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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