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- PDB-5z1z: The apo-structure of D-lactate dehydrogenase from Escherichia coli -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z1z | ||||||
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Title | The apo-structure of D-lactate dehydrogenase from Escherichia coli | ||||||
![]() | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | ||||||
![]() | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding | ||||||
Function / homology | ![]() mixed acid fermentation / D-lactate dehydrogenase / D-lactate dehydrogenase activity / NADH binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / response to heat / cytosol 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.8 KB | Display | ![]() |
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PDB format | ![]() | 400.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5z20C ![]() 5z21C ![]() 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: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 329 / Label seq-ID: 1 - 329
NCS ensembles :
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Components
#1: Protein | Mass: 36560.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 200 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2014 |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→48.24 Å / Num. obs: 90771 / % possible obs: 98.6 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11859 / CC1/2: 0.597 / Rpim(I) all: 0.325 / % possible all: 88.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J49 Resolution: 1.97→48.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.91 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.156 / 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: 38.602 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→48.24 Å
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Refine LS restraints |
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