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Yorodumi- PDB-1fcd: THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fcd | |||||||||
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Title | THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A PURPLE PHOTOTROPHIC BACTERIUM CHROMATIUM VINOSUM AT 2.5 ANGSTROMS RESOLUTION | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT(FLAVOCYTOCHROME) | |||||||||
Function / homology | Function and homology information sulfide-cytochrome-c reductase (flavocytochrome c) / flavin adenine dinucleotide binding / periplasmic space / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Allochromatium vinosum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.53 Å | |||||||||
Authors | Chen, Z.W. / Koh, M. / Van Driessche, G. / Van Beeumen, J.J. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Mathews, F.S. | |||||||||
Citation | Journal: Science / Year: 1994 Title: The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Authors: Chen, Z.W. / Koh, M. / Van Driessche, G. / Van Beeumen, J.J. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Mathews, F.S. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Nucleotide Sequence of the Heme Subunit of Flavocytochrome C from the Purple Phototrophic Bacterium, Chromatium Vinosum Authors: Dolata, M.M. / Van Beeumen, J.J. / Ambler, R.P. / Meyer, T.E. / Cusanovich, M.A. #2: Journal: Chemistry and Biochemistry of Flavoenzymes / Year: 1991 Title: Flavocytochrome C Authors: Cusanovich, M.A. / Meyer, T.E. / Bartsch, R.G. | |||||||||
History |
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Remark 650 | HELIX FLAVOPROTEIN SUBUNIT CONTAINS HELICES 1 - 22 IN *HELIX* RECORDS BELOW. CYTOCHROME SUBUNIT ...HELIX FLAVOPROTEIN SUBUNIT CONTAINS HELICES 1 - 22 IN *HELIX* RECORDS BELOW. CYTOCHROME SUBUNIT CONTAINS HELICES 23 - 38 IN *HELIX* RECORDS BELOW. | |||||||||
Remark 700 | SHEET THERE ARE TWO BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH ...SHEET THERE ARE TWO BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *A8* AND *A9* REPRESENT ONE BIFURCATED SHEET. SHEETS *B8* AND *B9* REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fcd.cif.gz | 231.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fcd.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fcd ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fcd | 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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Atom site foot note | 1: CIS PROLINE - PRO A 223 2: PHE A 400 - GLY A 401 OMEGA = 123.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO C 24 / 4: CIS PROLINE - PRO B 223 / 5: CIS PROLINE - PRO D 24 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.7707, 0.0185, -0.6369), Vector: Details | A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS EXISTS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *C* WHEN APPLIED TO CHAINS *B* AND *D*, RESPECTIVELY. | |
-Components
#1: Protein | Mass: 42844.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / References: UniProt: Q06530 #2: Protein | Mass: 19231.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / References: UniProt: Q06529 #3: Chemical | #4: Chemical | ChemComp-HEC / Compound details | THE ACTIVE SITE OF THE FLAVOPROTEIN SUBUNIT CONTAINS A CATALYTICALLY IMPORTANT DISULFIDE BRIDGE ...THE ACTIVE SITE OF THE FLAVOPROTE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.3 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.53 Å / % possible obs: 95 % |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.237 / Rfactor obs: 0.237 / Highest resolution: 2.53 Å Details: RESIDUES 1 - 174 OF THE CYTOCHROME SUBUNIT AND RESIDUES 1 - 95 OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM THE DNA SEQUENCE. RESIDUES 96 TO THE END OF THE FLAVOPROTEIN SUBUNIT WERE ...Details: RESIDUES 1 - 174 OF THE CYTOCHROME SUBUNIT AND RESIDUES 1 - 95 OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM THE DNA SEQUENCE. RESIDUES 96 TO THE END OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM PRELIMINARY PEPTIDE FRAGMENT SEQUENCES WHICH WERE ALIGNED BY CORRELATION WITH THE EXPERIMENTAL X-RAY MAP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.53 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.8 |