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Yorodumi- PDB-7dsp: Anthranilate phosphoribosyltransferase variant Ser121Ala from Sac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dsp | |||||||||
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Title | Anthranilate phosphoribosyltransferase variant Ser121Ala from Saccharomyces cerevisiae with Mg bound | |||||||||
Components | Anthranilate phosphoribosyltransferase | |||||||||
Keywords | TRANSFERASE / Glycosyltransferase / Tryptophan biosynthesis / anthranilate phosphoribosyltransferase activity | |||||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Wu, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae. Authors: Wu, X. / Zhang, M. / Kuang, Z. / Yue, J. / Xue, L. / Zhu, M. / Zhu, Z. / Khan, M.H. / Niu, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dsp.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dsp.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7dsp ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7dsp | HTTPS FTP |
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-Related structure data
Related structure data | 7dsjC 7dsmSC 7dsoC 7dsrC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 41823.773 Da / Num. of mol.: 2 / Mutation: S121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: TRP4, YDR354W, D9476.4 / Production host: Escherichia coli (E. coli) References: UniProt: P07285, anthranilate phosphoribosyltransferase #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: 2.18 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / Details: 18 % MPEG 5000, 0.1 M HEPES pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 55409 / % possible obs: 100 % / Redundancy: 13 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2737 / Rpim(I) all: 0.143 / Rrim(I) all: 0.517 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DSM Resolution: 1.95→46.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.275 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.138 / 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: 81.4 Å2 / Biso mean: 29.652 Å2 / Biso min: 18.94 Å2
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Refinement step | Cycle: final / Resolution: 1.95→46.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0
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