+Open data
-Basic information
Entry | Database: PDB / ID: 7uf8 | |||||||||
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Title | Structure of CtdP in complex with penicimutamide E and NADP+ | |||||||||
Components | CtdP | |||||||||
Keywords | OXIDOREDUCTASE / Diels-Alderase / oxidioreductase / NmrA-like | |||||||||
Function / homology | Penicimutamide E / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Function and homology information | |||||||||
Biological species | Penicillium citrinum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Rivera, S. / Liu, Z. / Newmister, S.A. / Gao, X. / Sherman, D.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat.Chem. / Year: 2023 Title: An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity. Authors: Liu, Z. / Rivera, S. / Newmister, S.A. / Sanders, J.N. / Nie, Q. / Liu, S. / Zhao, F. / Ferrara, J.D. / Shih, H.W. / Patil, S. / Xu, W. / Miller, M.D. / Phillips, G.N. / Houk, K.N. / Sherman, D.H. / Gao, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uf8.cif.gz | 601.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uf8.ent.gz | 414.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uf8_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7uf8_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7uf8_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 7uf8_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7uf8 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7uf8 | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39013.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium citrinum (fungus) / Gene: ctdP / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75 Details: 0.1 M BisTris pH 6.75, 25% PEG monomethyl ether 2000, 0.1 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.36 Å / Num. obs: 55814 / % possible obs: 99.8 % / Redundancy: 21.13 % / Biso Wilson estimate: 60.06 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.174 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 2.79 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 16814 / CC1/2: 0.826 / Rrim(I) all: 2.85 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→48.36 Å / SU ML: 0.3985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7196 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 72.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.36 Å
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Refine LS restraints |
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LS refinement shell |
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