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Yorodumi- PDB-6f4d: Structure of the Y21F variant of quinolinate synthase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f4d | ||||||
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Title | Structure of the Y21F variant of quinolinate synthase in complex with PGH | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Volbeda, A. / Fontecilla-Camps, J.C. | ||||||
Funding support | France, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA. Authors: Volbeda, A. / Saez Cabodevilla, J. / Darnault, C. / Gigarel, O. / Han, T.H. / Renoux, O. / Hamelin, O. / Ollagnier-de-Choudens, S. / Amara, P. / Fontecilla-Camps, J.C. #1: 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. #2: 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 | 6f4d.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f4d.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 6f4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f4d_validation.pdf.gz | 320.2 KB | Display | wwPDB validaton report |
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Full document | 6f4d_full_validation.pdf.gz | 320.5 KB | Display | |
Data in XML | 6f4d_validation.xml.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4d ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4d | HTTPS FTP |
-Related structure data
Related structure data | 6f48C 6f4lC 6g74C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34640.598 Da / Num. of mol.: 1 / Mutation: K219R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase |
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-Non-polymers , 5 types, 193 molecules
#2: Chemical | ChemComp-SF4 / | ||||
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#3: Chemical | ChemComp-PGH / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.41 Å3/Da / Density % sol: 49.05 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.1 Details: PEG33500, ammonium sulfate, oxaloacetate, DHAP, NaF, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→43.95 Å / Num. obs: 22406 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.064 / Rrim(I) all: 0.118 / Net I/σ(I): 10.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 2→39.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.788 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.174 Details: U VALUES : WITH TLS ADDED 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 max: 93.37 Å2 / Biso mean: 36.997 Å2 / Biso min: 21.57 Å2
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Refinement step | Cycle: final / Resolution: 2→39.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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