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Yorodumi- PDB-5fx2: COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fx2 | ||||||
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Title | COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Watt, W. / Watenpaugh, K.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures. Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D. #1: Journal: J.Biol.Chem. / Year: 1988 Title: Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Disulfovibrio Vulgaris (Hildenborough) Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P. #2: Journal: Flavins and Flavoproteins / Year: 1976 Title: A Crystallographic Structural Study of the Oxidation States of Desulfovibrio Vulgaris Flavodoxin Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #3: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN Year: 1975 Title: Flavin Mononucleotide Conformation and Environment in Flavodoxin from Desulfovibrio Vulgaris Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973 Title: The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0-Angstroms Resolution Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972 Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fx2.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fx2.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fx2_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 5fx2_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 5fx2_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 5fx2_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fx2 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fx2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15678.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / References: UniProt: P00323 |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.03 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 9999 Å / Num. all: 13516 / Num. obs: 9313 / Num. measured all: 53148 / Rmerge(I) obs: 0.08 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.213 / Highest resolution: 1.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 8694 / σ(I): 2 / Rfactor obs: 0.213 / Num. reflection all: 12471 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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