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Yorodumi- PDB-7xh4: Dihydrofolate Reductase-like Protein SacH in safracin biosynthesi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xh4 | ||||||
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Title | Dihydrofolate Reductase-like Protein SacH in safracin biosynthesis complex with safracin A | ||||||
Components | Uncharacterized protein sfcH | ||||||
Keywords | OXIDOREDUCTASE / reductase / safracin biosynthesis / self-resistance / complex structure. | ||||||
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 / Safracin A / Chem-NDP / Uncharacterized protein sfcH Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ma, X. / Shao, N. / Zhang, Y. / Yang, D. / 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 | 7xh4.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xh4.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xh4 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xh4 | HTTPS FTP |
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-Related structure data
Related structure data | 7xh2C 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-EN7 / |
#3: Chemical | ChemComp-NDP / |
#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: 2.44 Å3/Da / Density % sol: 49.49 % |
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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: 2.2→29.76 Å / Num. obs: 11851 / % possible obs: 99.7 % / Redundancy: 20 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 55.28 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.496 / Num. unique obs: 1186 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XW7 Resolution: 2.2→29.76 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.84 Å2 / Biso mean: 34.9333 Å2 / Biso min: 16.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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