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Yorodumi- PDB-2z8n: Structural basis for the catalytic mechanism of phosphothreonine lyase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8n | ||||||
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Title | Structural basis for the catalytic mechanism of phosphothreonine lyase | ||||||
Components | 27.5 kDa virulence protein | ||||||
Keywords | LYASE / short three-helix bundle / distorted beta-strand sheet | ||||||
Function / homology | Function and homology information Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chen, L. / Wang, H. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural basis for the catalytic mechanism of phosphothreonine lyase. Authors: Chen, L. / Wang, H. / Zhang, J. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z8n.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8n.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z8n_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2z8n_full_validation.pdf.gz | 458 KB | Display | |
Data in XML | 2z8n_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2z8n_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8n ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8n | HTTPS FTP |
-Related structure data
Related structure data | 2z8mC 2z8oSC 2z8pC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 27681.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: mkaD, spvC, vsdD / Plasmid: PGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A2M9 #2: Chemical | ChemComp-SO4 / #3: 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: 1.93 Å3/Da / Density % sol: 36.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 100mM Tris, 0.2mM ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 26, 2006 |
Radiation | Monochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→99 Å / Num. all: 39361 / Num. obs: 38881 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.66 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 9.8 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z8O Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 51.4676 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.83 Å
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