+Open data
-Basic information
Entry | Database: PDB / ID: 5f35 | |||||||||
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Title | Structure of quinolinate synthase in complex with citrate | |||||||||
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: 1.6 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: 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. / 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 | 5f35.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f35.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 5f35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f35_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 5f35_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 5f35_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5f35_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f35 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f35 | HTTPS FTP |
-Related structure data
Related structure data | 5f33C 5f3dC 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: 34656.598 Da / Num. of mol.: 1 / Mutation: 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-FLC / |
#4: Chemical | ChemComp-MG / |
#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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: PEG4000, Na3citrate, NH4acetate, NaCl, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→49.3 Å / Num. obs: 40043 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.57→1.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 1.6→27.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.345 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.081 / 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: 20.114 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.77 Å
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Refine LS restraints |
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