+Open data
-Basic information
Entry | Database: PDB / ID: 4ltd | |||||||||
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Title | Crystal structures of NADH:FMN oxidoreductase (EMOB) - apo form | |||||||||
Components | NADH-dependent FMN reductase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information alkanesulfonate catabolic process / FMN reductase (NAD(P)H) activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | EDTA-degrading bacterium BNC1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.186 Å | |||||||||
Authors | Nissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S. / Belchik, S.M. / Xun, L. / Kang, C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis. Authors: Nissen, M.S. / Youn, B. / Knowles, B.D. / Ballinger, J.W. / Jun, S.Y. / Belchik, S.M. / Xun, L. / Kang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ltd.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ltd.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 4ltd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ltd_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 4ltd_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 4ltd_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 4ltd_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4ltd ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4ltd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21115.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EDTA-degrading bacterium BNC1 (bacteria) Gene: emoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F9T2, FMN reductase (NADH) | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, ...Details: 10 mg/mL EmoB in 20 mM sodium acetate, pH 5, 1 mM EDTA, 1 mM DTT mixed with an equal volume of reservoir solution (0.1 M MES, pH 6.5, 1.6 M ammonium sulfate, 10% dioxane), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332, 0.97925, 0.97942, 0.91162 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2007 | |||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.186→24.241 Å / Num. all: 36423 / Num. obs: 17012 / Observed criterion σ(I): 2 | |||||||||||||||
Reflection shell | Highest resolution: 2.186 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.186→24.241 Å / SU ML: 0.18 / σ(F): 4.1 / Phase error: 15.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.186→24.241 Å
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Refine LS restraints |
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LS refinement shell |
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