+Open data
-Basic information
Entry | Database: PDB / ID: 8j0i | ||||||
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Title | Aldo-keto reductase KmAKR | ||||||
Components | NADPH-dependent alpha-keto amide reductase | ||||||
Keywords | OXIDOREDUCTASE / apo-form / NADPH-dependent / beta-8/alpha-8-barrel | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Kluyveromyces marxianus (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Aldo-keto reductase KmAKR from Kluyveromyces marxianus Authors: Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j0i.cif.gz | 259.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j0i.ent.gz | 210.4 KB | Display | PDB format |
PDBx/mmJSON format | 8j0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j0i_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 8j0i_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 8j0i_validation.xml.gz | 49.2 KB | Display | |
Data in CIF | 8j0i_validation.cif.gz | 70.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/8j0i ftp://data.pdbj.org/pub/pdb/validation_reports/j0/8j0i | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35429.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: KLMA_60481 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TDP7 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Sodium citrate tribasic dihydrate, TRIS hydrochloride, Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→56.15 Å / Num. obs: 95916 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.061 / Rrim(I) all: 0.155 / Χ2: 0.76 / Net I/σ(I): 7.7 / Num. measured all: 600337 |
Reflection shell | Resolution: 1.91→1.94 Å / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.25 / Num. measured all: 27254 / Num. unique obs: 4765 / CC1/2: 0.898 / Rpim(I) all: 0.115 / Rrim(I) all: 0.276 / Χ2: 0.37 / Net I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 1.91→56.15 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.872 / SU B: 3.739 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.75 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→56.15 Å
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Refine LS restraints |
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