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Yorodumi- PDB-1fcb: MOLECULAR STRUCTURE OF FLAVOCYTOCHROME B2 AT 2.4 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fcb | |||||||||
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Title | MOLECULAR STRUCTURE OF FLAVOCYTOCHROME B2 AT 2.4 ANGSTROMS RESOLUTION | |||||||||
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 / : / 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: 2.4 Å | |||||||||
Authors | Mathews, F.S. / Xia, Z.-X. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Molecular structure of flavocytochrome b2 at 2.4 A resolution. Authors: Xia, Z.X. / Mathews, F.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Three-Dimensional Structure of Flavocytochrome B2 from Baker,S Yeast at 3.0-Angstroms Resolution Authors: Xia, Z.-X. / Shamala, N. / Bethge, P.H. / Lim, L.W. / Bellamy, H.D. / Xuong, N.H. / Lederer, F. / Mathews, F.S. #2: Journal: J.Mol.Biol. / Year: 1976 Title: Crystallographic Study of Bakers, Yeast Cytochrome B2 Authors: Mathews, F.S. / Lederer, F. | |||||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *BRA* AND *BRB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BRA* AND *BRB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fcb.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fcb.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fcb_validation.pdf.gz | 633.1 KB | Display | wwPDB validaton report |
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Full document | 1fcb_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 1fcb_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 1fcb_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fcb ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fcb | 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: |
-Components
#1: Protein | Mass: 56663.898 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 | ChemComp-HEM / | #3: Chemical | #4: Chemical | ChemComp-PYR / | #5: Water | ChemComp-HOH / | Compound details | EACH SUBUNIT CONTAINS TWO DOMAINS, A CYTOCHROME DOMAIN COMPRISING RESIDUES 1 - 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: 3.96 Å3/Da / Density % sol: 68.98 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: microdialysis | |||||||||||||||||||||||||||||||||||||||||||||
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 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.4→5 Å Details: SOME BOND ANGLES DIFFER SIGNIFICANTLY FROM EXPECTED VALUES AND SOME RESIDUES FALL OUTSIDE THE ALLOWED REGIONS OF A PHI-PSI PLOT. FURTHER REFINEMENT IS IN PROGRESS AND REVISED COORDINATES ...Details: SOME BOND ANGLES DIFFER SIGNIFICANTLY FROM EXPECTED VALUES AND SOME RESIDUES FALL OUTSIDE THE ALLOWED REGIONS OF A PHI-PSI PLOT. FURTHER REFINEMENT IS IN PROGRESS AND REVISED COORDINATES WILL BE DEPOSITED WITH THE PROTEIN DATA BANK IN THE FUTURE.
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Refinement step | Cycle: LAST / Resolution: 2.4→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 61365 / Rfactor obs: 0.188 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |