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Yorodumi- PDB-6g74: Structure of the Y21F variant of quinolinate synthase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g74 | ||||||
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Title | Structure of the Y21F variant of quinolinate synthase in complex with phthalate | ||||||
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 / 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 | 6g74.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g74.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g74 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g74 | HTTPS FTP |
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-Related structure data
Related structure data | 6f48C 6f4dC 6f4lC 4p3xS 5lqmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34509.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG3350, TRIS, KCL, HEPES, PHTHALATE, Na2HPO4, ANAEROBIC |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→49.13 Å / Num. obs: 34665 / % possible obs: 90.2 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.044 / Rrim(I) all: 0.072 / Net I/σ(I): 12.1 / Num. measured all: 82582 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM) Resolution: 2→43.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.989 / SU ML: 0.172 / SU R Cruickshank DPI: 0.3231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.21 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: 78.59 Å2 / Biso mean: 31.326 Å2 / Biso min: 14.51 Å2
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Refinement step | Cycle: final / Resolution: 2→43.43 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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