+Open data
-Basic information
Entry | Database: PDB / ID: 2bkj | ||||||
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Title | NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI COMPLEXED WITH NAD+ | ||||||
Components | FLAVIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FRP | ||||||
Function / homology | Function and homology information FMN reductase (NADPH) / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / bioluminescence Similarity search - Function | ||||||
Biological species | Vibrio harveyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Tanner, J.J. / TU, S.-C. / Krause, K.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P. Authors: Tanner, J.J. / Tu, S.C. / Barbour, L.J. / Barnes, C.L. / Krause, K.L. #1: Journal: Biochemistry / Year: 1996 Title: Flavin Reductase P: Structure of a Dimeric Enzyme that Reduces Flavin Authors: Tanner, J.J. / Lei, B. / TU, S.C. / Krause, K.L. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary Crystallographic Analysis of Nadph:Fmn Oxidoreductase from Vibrio Harveyi Authors: Tanner, J. / Lei, B. / Liu, M. / TU, S.C. / Krause, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bkj.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkj.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bkj_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2bkj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2bkj_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2bkj_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkj ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkj | HTTPS FTP |
-Related structure data
Related structure data | 1bkjS S: Starting model for refinement |
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Similar structure data |
-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: (0.351634, -0.373835, -0.858255), Vector: |
-Components
#1: Protein | Mass: 26333.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: JM109 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q56691, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors #2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: Tanner, J., (1994) J.Mol.Biol., 241, 283. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 10, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→32 Å / Num. obs: 23598 / % possible obs: 84 % / Redundancy: 2.1 % / Rsym value: 0.034 |
Reflection shell | Resolution: 2.08→2.2 Å / % possible all: 38 |
Reflection | *PLUS Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 38 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BKJ Resolution: 2.08→32 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: PARAMETERS AND TOPOLOGY FILES FROM X-PLOR 3.851 DISTRIBUTION. FREE R VALUE TEST SET SELECTION IS THE SAME TEST SET THAT USED IN DETERMINATION OF PDB ENTRY 1BKJ.
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Refinement step | Cycle: LAST / Resolution: 2.08→32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.24 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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