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Yorodumi- PDB-3wbf: Crystal Structure of meso-diaminopimelate dehydrogenase from Symb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wbf | |||||||||
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Title | Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP | |||||||||
Components | Diaminopimelate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / domain motion / thermo-stable / d-amino acid dehydrogenase | |||||||||
Function / homology | Function and homology information diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotide binding Similarity search - Function | |||||||||
Biological species | Symbiobacterium thermophilum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å | |||||||||
Authors | Liu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M. | |||||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum. Authors: Liu, W. / Li, Z. / Huang, C.H. / Guo, R.T. / Zhao, L. / Zhang, D. / Chen, X. / Wu, Q. / Zhu, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wbf.cif.gz | 221 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wbf.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/3wbf ftp://data.pdbj.org/pub/pdb/validation_reports/wb/3wbf | HTTPS FTP |
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-Related structure data
Related structure data | 3wb9C 3wbbC 3bioS 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: 33312.410 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Symbiobacterium thermophilum (bacteria) Strain: T / IAM 14863 / Gene: meso-dapdh, STH1425 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67PI3, diaminopimelate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.74 Å3/Da / Density % sol: 55.07 % / Mosaicity: 0.932 ° |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MPD, PEG 6000, NADP+, DAP,, pH 7.5, vapor diffusion, sitting drop, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 25, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.12→50 Å / Num. all: 61605 / Num. obs: 61060 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.324 / Net I/σ(I): 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BIO Resolution: 2.12→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8134 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 60.4694 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 88.05 Å2 / Biso mean: 29.0927 Å2 / Biso min: 8.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→30 Å
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Refine LS restraints |
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Xplor file |
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