+Open data
-Basic information
Entry | Database: PDB / ID: 7kpq | ||||||
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Title | Crystal structure of CtdE in complex with FAD | ||||||
Components | FAD-dependent monooxygenase CtdE | ||||||
Keywords | BIOSYNTHETIC PROTEIN / FAD monooxygenase | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Penicillium citrinum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhao, B. / Hu, L. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Authors: Liu, Z. / Zhao, F. / Zhao, B. / Yang, J. / Ferrara, J. / Sankaran, B. / Venkataram Prasad, B.V. / Kundu, B.B. / Phillips Jr., G.N. / Gao, Y. / Hu, L. / Zhu, T. / Gao, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kpq.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kpq.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 7kpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/7kpq ftp://data.pdbj.org/pub/pdb/validation_reports/kp/7kpq | HTTPS FTP |
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-Related structure data
Related structure data | 7kptC 6pvhS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49786.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium citrinum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M calcium chloride dihydrate, 20% w/v PEG6000, 10% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2020 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.41 Å / Num. obs: 29584 / % possible obs: 99.64 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1468 / CC1/2: 0.762 / Rpim(I) all: 0.348 / % possible all: 98.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PVH Resolution: 2.1→34.41 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3078 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: 32.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→34.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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