+Open data
-Basic information
Entry | Database: PDB / ID: 7f7j | ||||||
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Title | The crystal structure of AKR4C17 | ||||||
Components | AKR4-2 | ||||||
Keywords | OXIDOREDUCTASE / Glyphosate resistance / GPJ degradation mechanism / aldo-keto reductase / structure-based engineering | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Echinochloa colona (corn panic grass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Li, H. / Yang, Y. / Hu, Y. / Chen, C.-C. / Huang, J.-W. / Min, J. / Dai, L. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: J Hazard Mater / Year: 2022 Title: Structural analysis and engineering of aldo-keto reductase from glyphosate-resistant Echinochloa colona Authors: Li, H. / Yang, Y. / Hu, Y. / Chen, C.C. / Huang, J.W. / Min, J. / Dai, L. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7j.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7j.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 7f7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f7j_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 7f7j_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 7f7j_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 7f7j_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7j ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7j | HTTPS FTP |
-Related structure data
Related structure data | 7f7kC 7f7lC 7f7mC 7w1wC 7w1xC 3h7uS 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: 35344.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinochloa colona (corn panic grass) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5J6VLZ7 #2: Chemical | ChemComp-CO / | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: 2.0 M Ammonium sulfate, 0.1 M MES pH 6.5 and 0.01 M CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97892 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→25 Å / Num. obs: 59007 / % possible obs: 94.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.042 / Rrim(I) all: 0.126 / Χ2: 2.358 / Net I/σ(I): 7.9 / Num. measured all: 458237 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H7U Resolution: 1.93→24.82 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.32 Å2 / Biso mean: 24.9985 Å2 / Biso min: 9.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→24.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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