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Yorodumi- PDB-5lqs: Structure of quinolinate synthase Y21F mutant in complex with sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lqs | |||||||||
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Title | Structure of quinolinate synthase Y21F mutant in complex with substrate-derived quinolinate | |||||||||
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, 1items
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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: The crystal structure of Fe4S4 quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad. Authors: Cherrier, M.V. / Chan, A. / Darnault, 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 | 5lqs.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lqs.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lqs_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 5lqs_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 5lqs_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5lqs_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lqs ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lqs | HTTPS FTP |
-Related structure data
Related structure data | 5f33C 5f35C 5f3dC 5lqmC 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: Y21F, 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-NTM / | ||
#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: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: PEG3350, ammonium sulfate, oxaloacetate, DHAP, NaCl, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979736 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979736 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.73 Å / Num. obs: 23026 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.551 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.854 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.143 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→40 Å
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Refine LS restraints |
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