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Yorodumi- PDB-7xh2: Dihydrofolate Reductase-like Protein SacH in safracin biosynthesis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xh2 | ||||||
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Title | Dihydrofolate Reductase-like Protein SacH in safracin biosynthesis | ||||||
Components | Uncharacterized protein sfcH | ||||||
Keywords | OXIDOREDUCTASE / reductase / safracin biosynthesis / self-resistance. | ||||||
Function / homology | 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / riboflavin biosynthetic process / Dihydrofolate reductase-like domain superfamily / Chem-NDP / Uncharacterized protein sfcH Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ma, X. / Shao, N. / Ma, M. / Tang, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Pharm Sin B / Year: 2023 Title: Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis. Authors: Shao, N. / Ma, X. / Zhang, Y.Y. / Yang, D. / Ma, M. / Tang, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xh2.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xh2.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xh2_validation.pdf.gz | 725.6 KB | Display | wwPDB validaton report |
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Full document | 7xh2_full_validation.pdf.gz | 728.7 KB | Display | |
Data in XML | 7xh2_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7xh2_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xh2 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xh2 | HTTPS FTP |
-Related structure data
Related structure data | 7xh4C 2xw7S 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
#1: Protein | Mass: 22018.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5JCL3 |
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#2: Chemical | ChemComp-NDP / |
#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: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 28% (w/v) PEG 1500, 100mM PCB buffer pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.84 Å / Num. obs: 5881 / % possible obs: 99 % / Redundancy: 20 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 46.87 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.261 / Num. unique obs: 589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XW7 Resolution: 2.8→29.84 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.791 / SU B: 17.867 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 77.88 Å2 / Biso mean: 30.536 Å2 / Biso min: 3.31 Å2
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Refinement step | Cycle: final / Resolution: 2.8→29.84 Å
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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