+Open data
-Basic information
Entry | Database: PDB / ID: 1dap | ||||||
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Title | C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ | ||||||
Components | DIAMINOPIMELIC ACID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NADP / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / ASYMMETRIC DIMER | ||||||
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 / MIR / Resolution: 2.2 Å | ||||||
Authors | Scapin, G. / Reddy, S.G. / Blanchard, J.S. | ||||||
Citation | 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. #1: 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 | 1dap.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dap.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dap_validation.pdf.gz | 562.5 KB | Display | wwPDB validaton report |
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Full document | 1dap_full_validation.pdf.gz | 590.1 KB | Display | |
Data in XML | 1dap_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1dap_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dap ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dap | HTTPS FTP |
-Related structure data
Similar structure data |
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-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) / Strain: KY 10755 / 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 | #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 grow | *PLUS Method: vapor diffusion, hanging dropDetails: Reddy, S.G., (1996) Proteins: Struct.,Funct., Genet., 25, 514. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Sep 20, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 36359 / % possible obs: 89.2 % / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.221 / % possible all: 64.8 |
Reflection | *PLUS Num. measured all: 135992 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 64.8 % / Num. unique obs: 4374 / Num. measured obs: 11329 / Rmerge(I) obs: 0.221 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |