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Yorodumi- PDB-5f3d: Structure of quinolinate synthase in complex with reaction interm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f3d | |||||||||
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Title | Structure of quinolinate synthase in complex with reaction intermediate W | |||||||||
Components | Quinolinate synthase A | |||||||||
Keywords | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | |||||||||
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: 1.9 Å | |||||||||
Authors | Volbeda, A. / Fontecilla-Camps, J.C. | |||||||||
Funding support | France, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product. Authors: Volbeda, A. / Darnault, C. / Renoux, O. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C. #1: Journal: J.AM.CHEM.SOC. / Year: 2014 Title: STRUCTURE OF THE FE4S4 QUINOLINATE SYNTHASE NADA FROM THERMOTOGA MARITIMA Authors: Cherrier, M.V. / Chan, A. / Darnaux, C. / Reichmann, D. / Amara, P. / 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 | 5f3d.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3d.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f3d_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 5f3d_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 5f3d_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5f3d_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3d ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3d | HTTPS FTP |
-Related structure data
Related structure data | 5f33C 5f35C 5lqmC 5lqsC 4p3xS 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 / Mutation: Y107F, K219R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase | ||
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#2: Chemical | ChemComp-SF4 / | ||
#3: Chemical | ChemComp-5UK / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG3350, Tris, LiSO4, NH4SO4, KCl, DHAP, oxaloacetic acid, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.2 Å / Num. obs: 23542 / % possible obs: 97 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.4 / % possible all: 89.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.543 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.946 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45 Å
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Refine LS restraints |
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