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Yorodumi- PDB-5f33: Structure of quinolinate synthase in complex with phosphoglycoloh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f33 | |||||||||
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Title | Structure of quinolinate synthase in complex with phosphoglycolohydroxamate | |||||||||
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: 1.45 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 | 5f33.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f33.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f33 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f33 | HTTPS FTP |
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-Related structure data
Related structure data | 5f35C 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: 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase | ||
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#2: Chemical | ChemComp-SF4 / | ||
#3: Chemical | ChemComp-PGH / | ||
#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: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: PEG3350, Tris, LiSO4, KCl, PGH anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96862 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.45→49.16 Å / Num. obs: 51724 / % possible obs: 98.6 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.034 / Net I/σ(I): 12 / Num. measured all: 143402 / Scaling rejects: 3 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066 / 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: 22.337 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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