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- PDB-5z21: The ternary structure of D-lactate dehydrogenase from Fusobacteri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z21 | ||||||
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Title | The ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH and oxamate | ||||||
![]() | D-lactate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Ternary complex / Rossmann Fold / Dehydrogenase / NADH binding | ||||||
Function / homology | ![]() D-lactate dehydrogenase / D-lactate dehydrogenase activity / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H. | ||||||
![]() | ![]() Title: Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Authors: Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.5 KB | Display | ![]() |
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PDB format | ![]() | 437.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5z1zC ![]() 5z20C ![]() 6abiC ![]() 6abjC ![]() 1j49S C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 40788.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN0511 / Plasmid: pColdI / Production host: ![]() ![]() #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-OXM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2 mM NADH, 25 mM oxamate, 100 mM acetate buffer pH 5, 4% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42.01 Å / Num. obs: 75787 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.05 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10924 / CC1/2: 0.738 / Rpim(I) all: 0.254 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J49 Resolution: 2.3→42.01 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.647 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.925 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→42.01 Å
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Refine LS restraints |
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