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Yorodumi- PDB-6hg6: Clostridium beijerinckii aldo-keto reductase Cbei_3974 with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hg6 | ||||||
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Title | Clostridium beijerinckii aldo-keto reductase Cbei_3974 with NADPH | ||||||
Components | L-glyceraldehyde 3-phosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / Aldo keto reductase / AKR / Clostridium beijerinckii / Cbei_3974 / aldehyde reductase / methylglyoxal / TIM barrel / NADPH / furfural resistance / 3D Structure determination | ||||||
Function / homology | Function and homology information D-threo-aldose 1-dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function | ||||||
Biological species | Clostridium beijerinckii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Scott, A.F. / Cresser-Brown, J. / Rizkallah, P.J. / Jin, Y. / Allemann, R.K. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2019 Title: Crystal Structure and Biophysical Analysis of Furfural-Detoxifying Aldehyde Reductase from Clostridium beijerinckii. Authors: Scott, A.F. / Cresser-Brown, J. / Williams, T.L. / Rizkallah, P.J. / Jin, Y. / Luk, L.Y. / Allemann, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hg6.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hg6.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hg6 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hg6 | HTTPS FTP |
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-Related structure data
Related structure data | 5t79S S: Starting model for refinement |
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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: 37285.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Gene: gpr_2, CBEIJ_11710 / Plasmid: pET-14b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1S8QGT2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor | ||
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#2: Chemical | ChemComp-NDP / | ||
#3: Chemical | ChemComp-EDO / #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: 3.18 Å3/Da / Density % sol: 61.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 90 mM MOPS pH 7.6, 271 mM NH4Cl2, 2.7% PEG 8K, 10 mM NADPH, 2 mM 4-pyridine methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→54.58 Å / Num. obs: 42762 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.094 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3169 / CC1/2: 0.725 / Rrim(I) all: 0.963 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T79 Resolution: 1.75→54.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.428 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.821 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→54.58 Å
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Refine LS restraints |
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