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Yorodumi- PDB-7qni: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qni | ||||||
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Title | CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V | ||||||
Components | Lactaldehyde reductase | ||||||
Keywords | OXIDOREDUCTASE / FucO / NADH / Dehydrogenase / aldehyde reductase | ||||||
Function / homology | Function and homology information lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / alcohol dehydrogenase (NAD+) activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics. Authors: Zavarise, A. / Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qni.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qni.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qni_validation.pdf.gz | 872 KB | Display | wwPDB validaton report |
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Full document | 7qni_full_validation.pdf.gz | 874.3 KB | Display | |
Data in XML | 7qni_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7qni_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/7qni ftp://data.pdbj.org/pub/pdb/validation_reports/qn/7qni | HTTPS FTP |
-Related structure data
Related structure data | 7qnfC 7qnjC 7r0pC 7r3dC 7r5tC 1rrmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 41521.277 Da / Num. of mol.: 1 / Mutation: L259V, S315G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: fucO, Z4116, ECs3659 / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.04 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M Sodium citrate, pH 5.6; 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 28, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→54.24 Å / Num. obs: 39368 / % possible obs: 100 % / Redundancy: 13.23 % / Biso Wilson estimate: 28.434 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2151 / CC1/2: 0.759 / Rpim(I) all: 0.494 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRM Resolution: 1.73→54.239 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.269 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.107 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.522 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→54.239 Å
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Refine LS restraints |
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LS refinement shell |
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