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Yorodumi- PDB-4gxm: OYE1-W116L in complex with aromatic product of R-carvone dismutation -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gxm | ||||||
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Title | OYE1-W116L in complex with aromatic product of R-carvone dismutation | ||||||
Components | NADPH dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / enoate reductase / OYE / carvone / enanatiocomplementarity / TIM barrel / FMN binding domain / NAD(P)H oxidoreductase / FMN NAD(P)H | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces pastorianus (lager yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.362 Å | ||||||
Authors | Pompeu, Y.A. / Stewart, J.D. | ||||||
Citation | Journal: ACS CATALYSIS / Year: 2013 Title: X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase Authors: Pompeu, Y.A. / Sullivan, B. / Stewart, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gxm.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gxm.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 4gxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gxm_validation.pdf.gz | 785.6 KB | Display | wwPDB validaton report |
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Full document | 4gxm_full_validation.pdf.gz | 788.5 KB | Display | |
Data in XML | 4gxm_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 4gxm_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/4gxm ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gxm | HTTPS FTP |
-Related structure data
Related structure data | 3txzC 4gbuSC 4ge8C 4gweC 4h6kC 4k7vC 4k7yC 4k8eC 4k8hC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44998.590 Da / Num. of mol.: 1 / Mutation: w116L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces pastorianus (lager yeast) Gene: OYE1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q02899, NADPH dehydrogenase |
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-Non-polymers , 7 types, 648 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-1PE / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-FMN / | #7: Chemical | ChemComp-0WV / | #8: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2M MgCl2, 0.1M Hepes, 35%PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 26, 2012 |
Radiation | Monochromator: si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 87102 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 16.5 % / Biso Wilson estimate: 13.08 Å2 / Rsym value: 0.062 / Net I/σ(I): 60.1 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.68 / Num. unique all: 2611 / Rsym value: 0.394 / % possible all: 56.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4gbu Resolution: 1.362→34.227 Å / SU ML: 0.08 / Cross valid method: 10% throughout / σ(F): 1.36 / Phase error: 11.16 / 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: 1.362→34.227 Å
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Refine LS restraints |
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LS refinement shell |
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