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Yorodumi- PDB-1ldc: X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ldc | |||||||||
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Title | X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE | |||||||||
Components | L-LACTATE DEHYDROGENASELactate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME | |||||||||
Function / homology | Function and homology information L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / lactate metabolic process / respirasome / mitochondrial intermembrane space / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | |||||||||
Authors | Tegoni, M. / Cambillau, C. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 Title: X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate. Authors: Tegoni, M. / Begotti, S. / Cambillau, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ldc.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ldc.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ldc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ldc ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ldc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: ALA A 148 - ASN A 149 OMEGA = 147.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY A 502 - PRO A 503 OMEGA = 148.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.25059, 0.43357, -0.86558), Vector: |
-Components
#1: Protein | Mass: 56647.898 Da / Num. of mol.: 2 / Mutation: Y143F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PGR / Plasmid: PGR 401 / Gene (production host): PGR / Production host: Escherichia coli (E. coli) References: UniProt: P00175, L-lactate dehydrogenase (cytochrome) #2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.68 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.5 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Jan 8, 1993 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 30412 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.15 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 100 Å / Num. measured all: 156473 / Rmerge(I) obs: 0.15 |
-Processing
Software |
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Refinement | Resolution: 2.9→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3.7 |