+Open data
-Basic information
Entry | Database: PDB / ID: 4b5n | ||||||
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Title | Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) | ||||||
Components | OXIDOREDUCTASE, FMN-BINDING | ||||||
Keywords | OXIDOREDUCTASE / COFACTOR-BINDING | ||||||
Function / homology | Function and homology information flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | SHEWANELLA ONEIDENSIS MR-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Elegheert, J. / Brige, A. / Savvides, S.N. | ||||||
Citation | Journal: FEBS Lett. / Year: 2017 Title: Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands. Authors: Elegheert, J. / Brige, A. / Van Beeumen, J. / Savvides, S.N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b5n.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b5n.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b5n_validation.pdf.gz | 946.9 KB | Display | wwPDB validaton report |
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Full document | 4b5n_full_validation.pdf.gz | 950.6 KB | Display | |
Data in XML | 4b5n_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 4b5n_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/4b5n ftp://data.pdbj.org/pub/pdb/validation_reports/b5/4b5n | HTTPS FTP |
-Related structure data
Related structure data | 5k0rC 5k1kC 5k1mC 5k1qC 5k1uC 5k1wC 2gouS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 39129.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA ONEIDENSIS MR-1 (bacteria) / Plasmid: PACYC-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EBV3, NADPH dehydrogenase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-8K6 / |
#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: 1.91 Å3/Da / Density % sol: 35.5 % / Description: NONE |
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Crystal grow | pH: 6.3 / Details: 1.6M SODIUM CITRATE TRIBASIC DIHYDRATE, PH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.85 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 120389 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 9.54 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GOU Resolution: 1.1→48.442 Å / SU ML: 0.08 / σ(F): 1.99 / Phase error: 12.07 / 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 / Bsol: 0 Å2 / ksol: 0 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→48.442 Å
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Refine LS restraints |
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LS refinement shell |
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