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Open data
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Basic information
Entry | Database: PDB / ID: 2dap | ||||||||||||
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Title | C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP | ||||||||||||
![]() | DIAMINOPIMELIC ACID DEHYDROGENASE | ||||||||||||
![]() | OXIDOREDUCTASE / DEHYDROGENASE / D-AMINO ACID DEHYDROGENASE / LYSINE BIOSYNTHESIS / DIAMINOPIMELATE | ||||||||||||
Function / homology | ![]() diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Scapin, G. / Cirilli, M. / Reddy, S.G. / Gao, Y. / Vederas, J.C. / Blanchard, J.S. | ||||||||||||
![]() | ![]() 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: ![]() Title: Three-Dimensional Structure of Meso-Diaminopimelic Acid Dehydrogenase from Corynebacterium Glutamicum Authors: Scapin, G. / Reddy, S.G. / Blanchard, J.S. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.9 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dapC ![]() 1dapS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 35242.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-API / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996 |
Radiation | Monochromator: NI FILTERS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 21456 / % possible obs: 94.8 % / Redundancy: 4 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.293 / % possible all: 82.3 |
Reflection | *PLUS Num. measured all: 86282 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS % possible obs: 82.3 % / Num. unique obs: 2297 / Num. measured obs: 7642 / Rmerge(I) obs: 0.293 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAP Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 23.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.195 / Rfactor obs: 0.192 / Rfactor Rwork: 0.17 / Num. reflection obs: 20794 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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