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Yorodumi- PDB-1ltd: THE 2.6 ANGSTROMS REFINED STRUCTURE OF THE ESCHERICHIA COLI RECOM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ltd | ||||||
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Title | THE 2.6 ANGSTROMS REFINED STRUCTURE OF THE ESCHERICHIA COLI RECOMBINANT SACCHAROMYCES CEREVISIAE FLAVOCYTOCHROME B2-SULPHITE COMPLEX | ||||||
Components | FLAVOCYTOCHROME B2 | ||||||
Keywords | OXIDOREDUCTASE(CH-OH(D)-CYTOCHROME(A)) | ||||||
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 / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: The 2.6-A refined structure of the Escherichia coli recombinant Saccharomyces cerevisiae flavocytochrome b2-sulfite complex. Authors: Tegoni, M. / Cambillau, C. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Molecular Structure of Flavocytochrome B2 at 2.4 Angstroms Resolution Authors: Xia, Z. / Mathews, F.S. #2: Journal: Biochem.J. / Year: 1989 Title: High Level Expression of Fully Active Yeast Flavocytochrome B2 in Escherichia Coli Authors: Black, M. / White, S. / Reid, G. / Chapman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ltd.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ltd.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ltd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ltd_validation.pdf.gz | 632.8 KB | Display | wwPDB validaton report |
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Full document | 1ltd_full_validation.pdf.gz | 678.2 KB | Display | |
Data in XML | 1ltd_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1ltd_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1ltd ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1ltd | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.247, 0.4353, -0.8657), Vector: Details | THE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. | |
-Components
#1: Protein | Mass: 56080.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00175, L-lactate dehydrogenase (cytochrome) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | Compound details | EACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 5 - 99 AND A FLAVIN- ...EACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 100 Å / Num. obs: 44282 / % possible obs: 81 % / Num. measured all: 452385 / Rmerge(I) obs: 0.147 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.9 Å / % possible obs: 55 % |
-Processing
Software |
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Refinement | Resolution: 2.6→6 Å / Rfactor Rwork: 0.173 / Rfactor obs: 0.173 / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.37 |