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Yorodumi- PDB-2q9j: Crystal structure of the C217S mutant of diaminopimelate epimerase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q9j | ||||||
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Title | Crystal structure of the C217S mutant of diaminopimelate epimerase | ||||||
Components | Diaminopimelate epimerase | ||||||
Keywords | ISOMERASE / C217S mutant / two domains / open conformation of the apo-enzyme | ||||||
Function / homology | Function and homology information diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pillai, B. / Cherney, M. / Diaper, C.M. / Sutherland, A. / Blanchard, J.S. / Vederas, J.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. Authors: Pillai, B. / Cherney, M. / Diaper, C.M. / Sutherland, A. / Blanchard, J.S. / Vederas, J.C. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q9j.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q9j.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2q9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q9j_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 2q9j_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 2q9j_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2q9j_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/2q9j ftp://data.pdbj.org/pub/pdb/validation_reports/q9/2q9j | HTTPS FTP |
-Related structure data
Related structure data | 2q9hC 1gqzS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30279.412 Da / Num. of mol.: 1 / Mutation: C217S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: dapF / Production host: Escherichia coli (E. coli) / References: UniProt: P44859, diaminopimelate epimerase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: (0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2005 / Details: double crystal |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 20304 / Num. obs: 20304 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.446 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQZ Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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