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- PDB-1ez4: CRYSTAL STRUCTURE OF NON-ALLOSTERIC L-LACTATE DEHYDROGENASE FROM ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ez4 | ||||||
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Title | CRYSTAL STRUCTURE OF NON-ALLOSTERIC L-LACTATE DEHYDROGENASE FROM LACTOBACILLUS PENTOSUS AT 2.3 ANGSTROM RESOLUTION | ||||||
![]() | LACTATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | ![]() L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Uchikoba, H. / Fushinobu, S. / Wakagi, T. / Konno, M. / Taguchi, H. / Matsuzawa, H. | ||||||
![]() | ![]() Title: Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces. Authors: Uchikoba, H. / Fushinobu, S. / Wakagi, T. / Konno, M. / Taguchi, H. / Matsuzawa, H. #1: ![]() Title: Unusual Amino Acid Substitution in the Anion-binding Site of Lactobacillus plantarum Non-allosteric L-lactate Dehydrogenase Authors: Taguchi, H. / Ohta, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262 KB | Display | ![]() |
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PDB format | ![]() | 212 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 57 KB | Display | |
Data in CIF | ![]() | 80 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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2 | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer constructed from chain A-D. The symmetry partners have three two-fold axes in total. |
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Components
#1: Protein | Mass: 34037.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.46 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ammonium sulfate, sodium acetate, NADH, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2.2→40 Å / Num. obs: 123693 / % possible obs: 99.3 % / Observed criterion σ(I): 0.1 / Redundancy: 8.7 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.3 | ||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.367 / Num. unique all: 286006 / % possible all: 96.7 | ||||||||||||
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 1078131 / Rmerge(I) obs: 0.125 |
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Processing
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Refinement | Resolution: 2.3→80 Å / σ(F): 2 / Stereochemistry target values: X-PLOR 3.851 param19.pro / Details: bulk solvent correction
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Refinement step | Cycle: LAST / Resolution: 2.3→80 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 80 Å / σ(F): 2 / Rfactor obs: 0.205 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |