+Open data
-Basic information
Entry | Database: PDB / ID: 7xft | |||||||||
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Title | MucP PDZ2 domain | |||||||||
Components | Putative zinc metalloprotease PA3649 | |||||||||
Keywords | LYASE / MucP / alginate biosynthesis / Pseudomonas aeruginosa PAO1 / Crystal structure. | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | |||||||||
Authors | Lou, X. / Li, S. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: MucP PDZ2 domain Authors: Lou, X. / Li, S. / Zhang, Q. / Bartlam, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xft.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xft.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xft_validation.pdf.gz | 741.5 KB | Display | wwPDB validaton report |
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Full document | 7xft_full_validation.pdf.gz | 741.5 KB | Display | |
Data in XML | 7xft_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 7xft_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/7xft ftp://data.pdbj.org/pub/pdb/validation_reports/xf/7xft | HTTPS FTP |
-Related structure data
Related structure data | 3id2S S: Starting model for refinement |
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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: 9341.611 Da / Num. of mol.: 1 / Fragment: PDZ2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3649 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q9HXY3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||||
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#2: Chemical | ChemComp-VAL / | ||||
#3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 8000, 0.1M sodium arsenate, 0.2M thiamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 27025 / % possible obs: 99.3 % / Redundancy: 12.7 % / Biso Wilson estimate: 13.24 Å2 / Rpim(I) all: 0.022 / Net I/σ(I): 48.2 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1320 / Rpim(I) all: 0.091 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ID2 Resolution: 1.21→24.66 Å / SU ML: 0.1134 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.2961 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→24.66 Å
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Refine LS restraints |
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LS refinement shell |
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