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Yorodumi- PDB-1f0x: CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f0x | ||||||
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Title | CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRANE RESPIRATORY ENZYME. | ||||||
Components | D-LACTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information D-lactate dehydrogenase (quinone) / D-lactate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor / lactate oxidation / anaerobic respiration / plasma membrane => GO:0005886 / quinone binding / aerobic respiration / respiratory electron transport chain / extrinsic component of cytoplasmic side of plasma membrane ...D-lactate dehydrogenase (quinone) / D-lactate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor / lactate oxidation / anaerobic respiration / plasma membrane => GO:0005886 / quinone binding / aerobic respiration / respiratory electron transport chain / extrinsic component of cytoplasmic side of plasma membrane / FAD binding / transmembrane transport / flavin adenine dinucleotide binding / electron transfer activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Dym, O. / Pratt, E.A. / Ho, C. / Eisenberg, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Authors: Dym, O. / Pratt, E.A. / Ho, C. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f0x.cif.gz | 217.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f0x.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f0x ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f0x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64706.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P06149, D-lactate dehydrogenase #2: Chemical | #3: 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: 2.01 Å3/Da / Density % sol: 38.7 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 4000, potassium phosphate, mercaptoethanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97851 / Wavelength: 0.97851, 0.97880, 0.97116 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→99 Å / Num. all: 136988 / Num. obs: 134385 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1 | ||||||||||||
Reflection shell | Resolution: 1.9→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Num. unique all: 9173 / % possible all: 96.1 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 95767 / % possible obs: 91.1 % / Num. measured all: 1154879 / Rmerge(I) obs: 0.081 |
-Processing
Software |
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Refinement | Resolution: 1.9→18 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→18 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. reflection obs: 76528 / σ(F): 0 / Rfactor obs: 0.201 / Rfactor Rfree: 0.245 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |