+Open data
-Basic information
Entry | Database: PDB / ID: 7qw4 | ||||||
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Title | Pden_5119 protein | ||||||
Components | NADPH-dependent FMN reductase | ||||||
Keywords | CYTOSOLIC PROTEIN / flavinreductase | ||||||
Function / homology | : / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / NADPH-dependent FMN reductase Function and homology information | ||||||
Biological species | Paracoccus denitrificans PD1222 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Kryl, M. / Sedlacek, V. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans . Authors: Kryl, M. / Sedlacek, V. / Kucera, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qw4.cif.gz | 671.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qw4.ent.gz | 532.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qw4_validation.pdf.gz | 622.7 KB | Display | wwPDB validaton report |
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Full document | 7qw4_full_validation.pdf.gz | 747.9 KB | Display | |
Data in XML | 7qw4_validation.xml.gz | 133.6 KB | Display | |
Data in CIF | 7qw4_validation.cif.gz | 175.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/7qw4 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/7qw4 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
-Components
#1: Protein | Mass: 20628.336 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans PD1222 (bacteria) Gene: Pden_5119 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A1BCD5 |
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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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM trisodium phosphate, 300 mM sodium chloride, 300 mM imidazole, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→49.1 Å / Num. obs: 65429 / % possible obs: 90.22 % / Redundancy: 2 % / Biso Wilson estimate: 81.63 Å2 / Rpim(I) all: 0.0603 / Net I/av σ(I): 2.26 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.06→3.14 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3022 / CC1/2: 0.794 / Rrim(I) all: 0.438 / % possible all: 57.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 3.1→48.75 Å / SU ML: 0.4076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5117 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.75 Å
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Refine LS restraints |
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LS refinement shell |
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