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Yorodumi- PDB-2z8p: Structural basis for the catalytic mechanism of phosphothreonine lyase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8p | ||||||
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Title | Structural basis for the catalytic mechanism of phosphothreonine lyase | ||||||
Components |
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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 | 2z8p.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8p.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z8p_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 2z8p_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 2z8p_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2z8p_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8p ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8p | HTTPS FTP |
-Related structure data
Related structure data | 2z8mC 2z8nC 2z8oSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27623.037 Da / Num. of mol.: 1 / Mutation: K136A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A2M9 |
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#2: Protein/peptide | ( Mass: 869.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
#3: 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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 17% PEG (MME) 2000, 100mM HEPES, pH 7.5, 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: Jan 22, 2007 |
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: 25249 / Num. obs: 25173 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 47.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 8.5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z8O Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 34.9473 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→1.82 Å
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