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Yorodumi- PDB-7p4m: Structure of the quinolinate synthase Y107F variant in an empty o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p4m | ||||||
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Title | Structure of the quinolinate synthase Y107F variant in an empty open form | ||||||
Components | Quinolinate synthase A | ||||||
Keywords | TRANSFERASE / NAD biosynthesis / Iron Sulfur cluster / active site cavity | ||||||
Function / homology | Function and homology information quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD biosynthetic process from aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Volbeda, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA. Authors: Basbous, H. / Volbeda, A. / Amara, P. / Rohac, R. / Martin, L. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p4m.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p4m.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 7p4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p4m_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7p4m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7p4m_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 7p4m_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p4m ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p4m | HTTPS FTP |
-Related structure data
Related structure data | 7p4pC 7p4qC 5f35S 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
#1: Protein | Mass: 34640.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: nadA, TM_1644 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | ChemComp-F3S / | ||||
#4: Chemical | #5: 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: 2.28 Å3/Da / Density % sol: 46.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaF, Bis Tris propane, anaerobic, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→49.05 Å / Num. obs: 44673 / % possible obs: 98.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.028 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.55→1.6 Å / Rmerge(I) obs: 0.498 / Num. unique obs: 4354 / CC1/2: 0.608 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F35 Resolution: 1.55→46.48 Å / SU ML: 0.1736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.557 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: 37.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→46.48 Å
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Refine LS restraints |
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LS refinement shell |
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