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Yorodumi- PDB-3dap: C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dap | ||||||
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Title | C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE | ||||||
Components | DIAMINOPIMELIC ACID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NADP / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / ASYMMETRIC DIMER / INHIBITOR | ||||||
Function / homology | Function and homology information diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Scapin, G. / Cirilli, M. / Reddy, S.G. / Gao, Y. / Vederas, J.C. / Blanchard, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. Authors: Scapin, G. / Cirilli, M. / Reddy, S.G. / Gao, Y. / Vederas, J.C. / Blanchard, J.S. #1: Journal: Biochemistry / Year: 1996 Title: Three-Dimensional Structure of Meso-Diaminopimelic Acid Dehydrogenase from Corynebacterium Glutamicum Authors: Scapin, G. / Reddy, S.G. / Blanchard, J.S. #2: Journal: Proteins / Year: 1996 Title: Expression, Purification, and Crystallization of Meso-Diaminopimelate Dehydrogenase from Corynebacterium Glutamicum Authors: Reddy, S.G. / Scapin, G. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dap.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dap.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dap_validation.pdf.gz | 938.1 KB | Display | wwPDB validaton report |
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Full document | 3dap_full_validation.pdf.gz | 952.8 KB | Display | |
Data in XML | 3dap_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 3dap_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dap ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dap | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35242.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Cell line: BL21 / Gene: DAPDH / Plasmid: PET23A / Species (production host): Escherichia coli / Gene (production host): DAPDH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04964, diaminopimelate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-DA3 / ( | #4: 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: 2.8 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 13-17% PEG 8000 IN 100 MM NA-CACODYLATE, PH 6.5, 150-300 MM MG-ACETATE CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1997 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→19 Å / Num. obs: 46303 / % possible obs: 88.9 % / Redundancy: 2 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.209 / % possible all: 77.7 |
Reflection | *PLUS Num. measured all: 70458 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 77.7 % / Num. unique obs: 4342 / Num. measured obs: 5440 / Rmerge(I) obs: 0.209 |
-Processing
Software |
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Refinement | Resolution: 2.2→19 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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