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Open data
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Basic information
Entry | Database: PDB / ID: 2j6i | ||||||
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Title | Candida boidinii formate dehydrogenase (FDH) C-terminal mutant | ||||||
![]() | FORMATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / D-SPECIFIC-2- HYDROXY ACID DEHYDROGENASE / NAD+ DEPENDENT FORMATE DEHYDROGENASE / COFACTOR REGENERATOR / YEAST / CBFDH / CANDIDA BOIDINII | ||||||
Function / homology | ![]() NADH regeneration / formate dehydrogenase complex / methanol oxidation / formate catabolic process / methylamine metabolic process / formate dehydrogenase / choline catabolic process / formate dehydrogenase (NAD+) activity / NADH metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...NADH regeneration / formate dehydrogenase complex / methanol oxidation / formate catabolic process / methylamine metabolic process / formate dehydrogenase / choline catabolic process / formate dehydrogenase (NAD+) activity / NADH metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding / protein homodimerization activity / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schirwitz, K. / Schmidt, A. / Lamzin, V.S. | ||||||
![]() | ![]() Title: High-Resolution Structures of Formate Dehydrogenase from Candida Boidinii. Authors: Schirwitz, K. / Schmidt, A. / Lamzin, V.S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.8 KB | Display | ![]() |
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PDB format | ![]() | 264.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 338.4 KB | Display | ![]() |
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Full document | ![]() | 408.3 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fssC ![]() 2nacS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 40189.656 Da / Num. of mol.: 4 Fragment: COFACTOR BINDING DOMAIN, CATALYTIC DOMAIN, RESIDUES 2-364 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) 70034 Plasmid: PTRCHIS2 / Production host: ![]() ![]() References: UniProt: O93968, UniProt: O13437*PLUS, formate dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 328 TO VAL ENGINEERED RESIDUE IN CHAIN B, LYS 328 TO VAL ...ENGINEERED | Sequence details | INITIAL METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 6 Details: 0.1 M SODIUM-CACODYLATE PH 6.0 0.2 M AMMONIUM-SULPHATE 32.5 % W/V PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8031 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→19.5 Å / Num. obs: 196828 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.55→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NAC Resolution: 1.55→19.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.378 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES GLY C 50 AND GLY D 50 ARE DISORDERED. RESIDUES 353-364 ARE MISSING IN THE ELECTRON DENSITY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→19.26 Å
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Refine LS restraints |
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