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Yorodumi- PDB-7xgm: Quinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xgm | ||||||
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Title | Quinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyces pyridomyceticus NRRL B-2517 in complex with Quinolinic Acid (QA) | ||||||
Components | Quinolinate Phosphoribosyl Transferase | ||||||
Keywords | TRANSFERASE / nicotinamide adenine dinucleotide / pyridomycin / quinolinic acid | ||||||
Function / homology | QUINOLINIC ACID Function and homology information | ||||||
Biological species | Streptomyces pyridomyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Zhou, Z. / Yang, X. / Huang, T. / Wang, X. / Liang, R. / Zheng, J. / Dai, S. / Lin, S. / Deng, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis. Authors: Zhou, Z. / Yang, X. / Huang, T. / Zheng, J. / Deng, Z. / Dai, S. / Lin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xgm.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xgm.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xgm ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgm | HTTPS FTP |
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-Related structure data
Related structure data | 7xglC 7xgnC 1qpoS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32412.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces pyridomyceticus (bacteria) Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 39 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.75 Å3/Da / Density % sol: 67.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Citric acid, pH 5.0, 1.6M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 193 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: Jun 18, 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: 2.85→19.13 Å / Num. obs: 23442 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.79 Å2 / CC1/2: 0.99 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.85→2.98 Å / Num. unique obs: 1164 / CC1/2: 0.903 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QPO Resolution: 2.85→19.13 Å / SU ML: 0.3885 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0663 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: 46.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→19.13 Å
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Refine LS restraints |
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LS refinement shell |
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