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Yorodumi- PDB-8ozv: Imine Reductase from Ajellomyces dermatitidis in complex with 2,2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ozv | ||||||
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Title | Imine Reductase from Ajellomyces dermatitidis in complex with 2,2-difluoroacetophenone | ||||||
Components | Oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Imine reductase / Amine / Dehydrogenase / NADP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Blastomyces dermatitidis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Sharma, M. / Grogan, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms. Authors: Sharma, M. / Cuetos, A. / Willliams, A. / Gonzalez-Martinez, D. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ozv.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ozv.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ozv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ozv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8ozv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8ozv_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 8ozv_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/8ozv ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8ozv | HTTPS FTP |
-Related structure data
Related structure data | 8ozwC 8p2jC 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: 30128.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastomyces dermatitidis (fungus) / Gene: BDBG_03427 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179UH34 |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-W65 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 100 mM PO4 buffer pH 8.6; 0.2 M MgCl2; 20% (w/v) PEG 3350; 2M NADP+; 10 mM ligand |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→42.22 Å / Num. obs: 55313 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.014 / Net I/σ(I): 52.1 |
Reflection shell | Resolution: 1.52→1.55 Å / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 24 / Num. unique obs: 2742 / CC1/2: 1 / Rpim(I) all: 0.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→42.22 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.735 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / 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: 12.842 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→42.22 Å
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Refine LS restraints |
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