+Open data
-Basic information
Entry | Database: PDB / ID: 4laf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PnpB complex with FMN | ||||||
Components | NAD(P)H dehydrogenase (quinone)NAD(P)H dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE / para-benzoquinone reductase / PnpB in complex with FMN | ||||||
Function / homology | Function and homology information p-benzoquinone reductase (NADPH) / p-benzoquinone reductase (NADPH) activity / 4-nitrophenol catabolic process / NAD(P)H dehydrogenase (quinone) activity / : / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å | ||||||
Authors | Su, J. / Zhang, C. / Li, N. / Gu, L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of PnpB complex with FMN Authors: Su, J. / Zhang, C. / Li, N. / Gu, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4laf.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4laf.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 4laf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4laf ftp://data.pdbj.org/pub/pdb/validation_reports/la/4laf | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22061.021 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: WBC-3 / Gene: pnpB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C1I202, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-FMN / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES monohydrate pH6.0, 20% Polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010 | |||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.76→50 Å / Num. all: 80299 / Num. obs: 80299 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 16.83 Å2 | |||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.761→35.633 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8687 / SU ML: 0.2 / σ(F): 0.08 / Phase error: 21.04 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.979 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.57 Å2 / Biso mean: 20.086 Å2 / Biso min: 7.68 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.761→35.633 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|