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- PDB-1xdw: NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidamin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xdw | ||||||
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Title | NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans | ||||||
![]() | NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / structural variant of the bab Rossmann fold | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martins, B.M. / Macedo-Ribeiro, S. / Bresser, J. / Buckel, W. / Messerschmidt, A. | ||||||
![]() | ![]() Title: Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans. Authors: Martins, B.M. / Macedo-Ribeiro, S. / Bresser, J. / Buckel, W. / Messerschmidt, A. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein has not been deposited into any sequence database. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.4 KB | Display | ![]() |
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PDB format | ![]() | 64.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.2 KB | Display | ![]() |
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Full document | ![]() | 405.3 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36631.152 Da / Num. of mol.: 1 / Fragment: HGDH Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15-18 % PEG MME 2000 or PEG 2000, and 0.2 M sodium or lithium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2002 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.98→20 Å / Num. all: 30959 / Num. obs: 28589 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.2 % / Biso Wilson estimate: 20.99 Å2 / Rsym value: 0.053 / Net I/σ(I): 28.17 | ||||||||||||
Reflection shell | Resolution: 1.98→2.031 Å / Mean I/σ(I) obs: 6.84 / Num. unique all: 1728 / Rsym value: 0.316 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.999 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→19.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20 /
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