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- PDB-1j49: INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j49 | ||||||
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Title | INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS | ||||||
![]() | D-LACTATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / NAD-DEPENDENT DEHYDROGENASE / LAST STEP OF GLYCOLYSIS UNDER ANAEROBIC CONDITIONS / REVERSIBLE INTERCONVERSION OF PYRUVATE INTO D-LACTATE | ||||||
Function / homology | ![]() D-lactate dehydrogenase / D-lactate dehydrogenase activity / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Razeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S. | ||||||
![]() | ![]() Title: Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus. Authors: Razeto, A. / Kochhar, S. / Hottinger, H. / Dauter, M. / Wilson, K.S. / Lamzin, V.S. | ||||||
History |
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Remark 999 | SEQUENCE The authors maintain that their sequence is correct. The density for these residues ...SEQUENCE The authors maintain that their sequence is correct. The density for these residues suggests ILE59, ARG117, AND VAL152 instead of those in the database reference match. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.3 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 969 KB | Display | ![]() |
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Full document | ![]() | 1008 KB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j4aC ![]() 2dldS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.31073, -0.06203, 0.94847), Vector: |
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Components
#1: Protein | Mass: 37121.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Lactobacillus delbrueckii / Strain: N42 Description: NESTLE CULTURE COLLECTION. PCR AMPLIFIED LDHA GENE Cellular location: CYTOPLASM / Gene: LDHA / Plasmid: PKBULDH / Cellular location (production host): CYTOPLASM / Gene (production host): LDHA / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 38147 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.73 / % possible all: 93.3 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 93.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DLD Resolution: 2.2→15 Å / SU B: 4.35 / SU ML: 0.11 Cross valid method: THROUGHOUT (EXCEPT FOR THE LAST 2 REFINEMENT CYCLES) σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.24
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Displacement parameters | Biso mean: 44.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |