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Yorodumi- PDB-2p1w: structure of the phosphothreonine lyase SpvC, the effector protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p1w | ||||||
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Title | structure of the phosphothreonine lyase SpvC, the effector protein from Salmonella | ||||||
Components | 27.5 kDa virulence protein | ||||||
Keywords | LYASE / beta sheet- alpha helix | ||||||
Function / homology | Function and homology information Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella enteritidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Zhu, Y. / Wang, D.C. / Shao, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase. Authors: Zhu, Y. / Li, H. / Long, C. / Hu, L. / Xu, H. / Liu, L. / Chen, S. / Wang, D.C. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p1w.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p1w.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p1w_validation.pdf.gz | 422 KB | Display | wwPDB validaton report |
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Full document | 2p1w_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 2p1w_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2p1w_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1w ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28876.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enteritidis (bacteria) / Gene: SpvC / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P0A2N1, Lyases; Carbon-oxygen lyases |
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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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG3350, 0.1M TrisHCl pH8.0, 5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9794 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 23, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 15486 / Num. obs: 15052 / % possible obs: 97.2 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.08 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 23.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 30 / Num. unique all: 1806 / Rsym value: 0.378 / % possible all: 72.2 |
-Phasing
Phasing | Method: SAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing dm | FOM : 0.63 / FOM acentric: 0.64 / FOM centric: 0.59 / Reflection: 13546 / Reflection acentric: 11435 / Reflection centric: 2111 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→50 Å / σ(F): 0
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Solvent computation | Bsol: 30.949 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.698 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Xplor file |
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