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Yorodumi- PDB-7r0p: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r0p | ||||||
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Title | CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I COMPLEXED WITH FE, NAD+, AND ETHYLENE GLYCOL | ||||||
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: 1.6 Å | ||||||
Authors | Shruthi, S. / Tiila, R.K. / Rikkert, W. / Mikael, W. | ||||||
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 | 7r0p.cif.gz | 310.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r0p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/7r0p ftp://data.pdbj.org/pub/pdb/validation_reports/r0/7r0p | HTTPS FTP |
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-Related structure data
Related structure data | 7qnfC 7qniC 7qnjC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 3 - 386 / Label seq-ID: 3 - 386
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 41531.320 Da / Num. of mol.: 2 / Mutation: F254I 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 str. K-12 substr. MG1655 (bacteria) Strain (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M Sodium acetate pH 4.5, 15% w/v PEG 3350, 0.25M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.77 Å / Num. obs: 98360 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 12.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.036 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 10.77 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4837 / CC1/2: 0.854 / Rpim(I) all: 0.309 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRM Resolution: 1.6→42.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.534 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.076 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: 17.241 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.77 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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