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Yorodumi- PDB-7v4p: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v4p | ||||||
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Title | Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction | ||||||
Components | Beta-hydroxylase | ||||||
Keywords | ANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase | ||||||
Function / homology | Isopenicillin N synthase-like superfamily / metal ion binding / : / Beta-hydroxylase Function and homology information | ||||||
Biological species | Streptomyces sp. MK730-62F2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Li, T.L. / Saeid, M.Z. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Commun Chem / Year: 2022 Title: beta-Hydroxylation of alpha-amino-beta-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin Authors: Zadeh, S.M. / Chen, M.H. / Wang, Z.C. / Astani, E.K. / Lo, I.W. / Lin, K.H. / Hsu, N.S. / Adhikari, K. / Lyu, S.Y. / Tsai, H.Y. / Terasawa, Y. / Yabe, M. / Yamamoto, K. / Ichikawa, S. / Li, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v4p.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v4p.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v4p_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7v4p_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7v4p_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7v4p_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/7v4p ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v4p | HTTPS FTP |
-Related structure data
Related structure data | 7v4fC 7v4mC 7v4nC 7v4oC 4p7xS 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: 22717.574 Da / Num. of mol.: 2 / Mutation: D117A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. MK730-62F2 (bacteria) / Gene: cpz10 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1 (others) References: UniProt: C4NCJ7 #2: Chemical | #3: 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: 2.08 Å3/Da / Density % sol: 36.3 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium acetate 0.1M Bis Tris propane pH 6.5 20 % W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→26.46 Å / Num. obs: 26710 / % possible obs: 100 % / Redundancy: 15.7 % / CC1/2: 0.939 / Net I/σ(I): 36.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 26733 / CC1/2: 0.939 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4p7x Resolution: 1.95→26.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→26.46 Å
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Refine LS restraints |
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LS refinement shell |
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