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Yorodumi- PDB-1lco: X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lco | ||||||
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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 DEHYDROGENASE | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase (cytochrome) / L-lactate dehydrogenase (cytochrome) activity / lactate metabolic process / : / mitochondrial intermembrane space / mitochondrial inner membrane / heme binding / mitochondrion / nucleus / metal ion binding / 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. #1: Journal: Protein Sci. / Year: 1994 Title: The 2.6-Angstroms Refined Structure of the Escherichia Coli Recombinant Saccharomyces Cerevisiae Flavocytochrome B2-Sulfite Complex Authors: Tegoni, M. / Cambillau, C. #2: Journal: Biochimie / Year: 1994 Title: Structural Studies on Recombinant and Point Mutants of Flavocytochrome B2 Authors: Tegoni, M. / Cambillau, C. #3: Journal: Proteins / Year: 1993 Title: A Hypothetical Complex between Crystalline Flavocytochrome B2 and Cytochrome C Authors: Tegoni, M. / White, S.A. / Roussel, A. / Mathews, F.S. / Cambillau, C. #4: Journal: Biochem.J. / Year: 1992 Title: Tyr-143 Facilitates Interdomain Electron Transfer in Flavocytochrome B2 Authors: Miles, C.S. / Rouviere-Fourmy, N. / Lederer, F. / Mathews, F.S. / Reid, G.A. / Black, M.T. / Chapman, S.K. #5: Journal: Biochem.J. / Year: 1989 Title: High-Level Expression of Fully Active Yeast Cytochrome B2 in Escherichia Coli Authors: Black, M.T. / White, S.A. / Reid, G. / Chapman, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lco.cif.gz | 228.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lco.ent.gz | 182.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lco_validation.pdf.gz | 634.2 KB | Display | wwPDB validaton report |
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Full document | 1lco_full_validation.pdf.gz | 687.1 KB | Display | |
Data in XML | 1lco_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 1lco_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lco ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lco | HTTPS FTP |
-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: ASP A 150 - GLU A 151 OMEGA = 147.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.260408, 0.466779, 0.845166), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 102 .. A 296 B 102 .. B 296 2.079 M1 A 321 .. A 511 B 321 .. B 511 2.357 | |
-Components
#1: Protein | Mass: 56647.898 Da / Num. of mol.: 2 / Mutation: TYR 143 PHE 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) / Strain (production host): MM294 References: UniProt: P00175, L-lactate dehydrogenase (cytochrome) #2: Chemical | ChemComp-HEM / | #3: Chemical | #4: Chemical | #5: 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: 3.93 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
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 35569 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 100 Å / Num. measured all: 263169 / Rmerge(I) obs: 0.13 |
-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: 3.5 |