+Open data
-Basic information
Entry | Database: PDB / ID: 1bkj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | NADPH:FMN OXIDOREDUCTASE FROM VIBRIO HARVEYI | |||||||||
Components | NADPH-FLAVIN OXIDOREDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE / LUMINESCENCE / NADP / FLAVOPROTEIN | |||||||||
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 / MIR / Resolution: 1.8 Å | |||||||||
Authors | Tanner, J.J. / Lei, B. / TU, S.-C. / Krause, K.L. | |||||||||
Citation | 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. #1: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bkj.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bkj.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bkj_validation.pdf.gz | 520.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bkj_full_validation.pdf.gz | 527.1 KB | Display | |
Data in XML | 1bkj_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1bkj_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkj ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkj | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.351799, -0.317456, -0.880601), 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 / Gene: VIBRIO HARVEYI NADPH\:FMN OXIDOREDUCTASE / Plasmid: PFRP1 / 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 | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / 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: 1.8→28 Å / Num. obs: 36163 / % possible obs: 82 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 40.7 |
Reflection | *PLUS Num. measured all: 117092 |
Reflection shell | *PLUS % possible obs: 40.7 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.8→28 Å / Data cutoff low absF: 1.3 / Cross valid method: THROUGHOUT Details: FMN, PO4 AND WATER PARAMETERS FROM X-PLOR 3.1 DISTRIBUTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|