+Open data
-Basic information
Entry | Database: PDB / ID: 1vfr | ||||||
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Title | THE MAJOR NAD(P)H:FMN OXIDOREDUCTASE FROM VIBRIO FISCHERI | ||||||
Components | NAD(P)H\:FMN OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NAD(P)H / FMN / VIBRIO FISCHERI / BIOLUMINESCENCE | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / bioluminescence / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Aliivibrio fischeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Koike, H. / Sasaki, H. / Kobori, T. / Zenno, S. / Saigo, K. / Murphy, M.E.P. / Adman, E.T. / Tanokura, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: 1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins. Authors: Koike, H. / Sasaki, H. / Kobori, T. / Zenno, S. / Saigo, K. / Murphy, M.E. / Adman, E.T. / Tanokura, M. #1: Journal: J.Struct.Biol. / Year: 1996 Title: Crystallization and Preliminary Crystallographic Analysis of the Major Nad(P)H: Fmn Oxidoreductase of Vibrio Fischeri Atcc 7744 Authors: Koike, H. / Sasaki, H. / Tanokura, M. / Zenno, S. / Saigo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfr.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfr.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vfr_validation.pdf.gz | 521.5 KB | Display | wwPDB validaton report |
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Full document | 1vfr_full_validation.pdf.gz | 528 KB | Display | |
Data in XML | 1vfr_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1vfr_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfr ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfr | 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: (-0.408754, 0.030328, 0.912141), Vector: |
-Components
#1: Protein | Mass: 24755.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 105 References: UniProt: P46072, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. obs: 40445 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.79→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.6 / % possible all: 74.4 |
Reflection | *PLUS Num. obs: 39895 / Num. measured all: 180543 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.27 |