+Open data
-Basic information
Entry | Database: PDB / ID: 1a5z | ||||||
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Title | LACTATE DEHYDROGENASE FROM THERMOTOGA MARITIMA (TMLDH) | ||||||
Components | L-LACTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GLYCOLYSIS / HYPERTHERMOPHILES / THERMOTOGA MARITIMA / PROTEIN STABILITY | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Auerbach, G. / Ostendorp, R. / Prade, L. / Korndoerfer, I. / Dams, T. / Huber, R. / Jaenicke, R. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Lactate dehydrogenase from the hyperthermophilic bacterium thermotoga maritima: the crystal structure at 2.1 A resolution reveals strategies for intrinsic protein stabilization. Authors: Auerbach, G. / Ostendorp, R. / Prade, L. / Korndorfer, I. / Dams, T. / Huber, R. / Jaenicke, R. #1: Journal: Protein Sci. / Year: 1996 Title: Extremely Thermostable L(+)-Lactate Dehydrogenase from Thermotoga Maritima: Cloning, Characterization, and Crystallization of the Recombinant Enzyme in its Tetrameric and Octameric State Authors: Ostendorp, R. / Auerbach, G. / Jaenicke, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a5z.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5z.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1a5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a5z_validation.pdf.gz | 598.4 KB | Display | wwPDB validaton report |
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Full document | 1a5z_full_validation.pdf.gz | 610.7 KB | Display | |
Data in XML | 1a5z_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1a5z_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5z ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5z | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 35026.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P16115, L-lactate dehydrogenase |
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#2: Sugar |
-Non-polymers , 4 types, 349 molecules
#3: Chemical | #4: Chemical | ChemComp-OXM / | #5: Chemical | ChemComp-NAD / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 30205 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.089 |
Reflection | *PLUS % possible obs: 97.9 % / Num. measured all: 111661 |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 35.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |