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Yorodumi- PDB-6kbl: Structure-function study of AKR4C14, an aldo-keto reductase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kbl | ||||||
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Title | Structure-function study of AKR4C14, an aldo-keto reductase from Thai Jasmine rice (Oryza sativa L. ssp. Indica cv. KDML105) | ||||||
Components | Aldo-keto reductase | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase (AKR) / Aldehyde reductase / Aldose reductase / rice AKR / AKR4C14 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Oryza sativa subsp. indica (long-grained rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Songsiriritthigul, C. / Narawongsanont, R. / Guan, H.H. / Chen, C.J. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structure-function study of AKR4C14, an aldo-keto reductase from Thai jasmine rice (Oryza sativa L. ssp. indica cv. KDML105). Authors: Songsiriritthigul, C. / Narawongsanont, R. / Tantitadapitak, C. / Guan, H.H. / Chen, C.J. #1: Journal: Protein J. / Year: 2017 Title: Characterization of AKR4C15, a Novel Member of Aldo-Keto Reductase, in Comparison with Other Rice AKR(s). Authors: Auiyawong, B. / Narawongsanont, R. / Tantitadapitak, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kbl.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kbl.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kbl_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 6kbl_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 6kbl_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6kbl_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/6kbl ftp://data.pdbj.org/pub/pdb/validation_reports/kb/6kbl | HTTPS FTP |
-Related structure data
Related structure data | 3h7uS 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: 34725.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice) Gene: AKR2, OsI_04428 / Plasmid: PET28B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8AC38 |
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#2: Chemical | ChemComp-CAC / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | The amino acid residue translated from gene is Glu74. But the amino acid that be properly rebuilt ...The amino acid residue translated from gene is Glu74. But the amino acid that be properly rebuilt in the map is Ala74 (appeared in the PDB Coordinates), owing to the disorder of its side chain. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % / Description: Rectangular morphology |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.5 Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 6.5, 30%(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2016 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 33541 / % possible obs: 99.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 18.28 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 4.53 / Num. unique obs: 1639 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H7U Resolution: 1.7→29.24 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 20.936 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.24 Å
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LS refinement shell | Resolution: 1.7→1.74 Å
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