[English] 日本語
Yorodumi- PDB-6f48: Structure of quinolinate synthase with reaction intermediates X and Y -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f48 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of quinolinate synthase with reaction intermediates X and Y | ||||||
Components | Quinolinate synthase A | ||||||
Keywords | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | ||||||
Function / homology | Function and homology information 'de novo' NAD biosynthetic process from aspartate / quinolinate synthase / quinolinate synthetase A activity / 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: 1.5 Å | ||||||
Authors | Volbeda, A. / Fontecilla-Camps, J.C. | ||||||
Funding support | France, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f48.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f48.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 6f48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f48_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6f48_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6f48_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6f48_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/6f48 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f48 | HTTPS FTP |
-Related structure data
Related structure data | 6f4dC 6f4lC 6g74C 4p3xS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#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 (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase |
---|
-Non-polymers , 6 types, 320 molecules
#2: Chemical | ChemComp-SF4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-XQB / | ||||
#4: Chemical | ChemComp-GOL / | ||||
#5: Chemical | #6: Chemical | ChemComp-YQA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.1 Details: PEG33500, ammonium sulfate, oxaloacetate, DHAP, NaF, Bis Tris propane, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→37.54 Å / Num. obs: 49728 / % possible obs: 98.8 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 16.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P3X Resolution: 1.5→37.5 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 4.812 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.067 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.8 Å2 / Biso mean: 27.231 Å2 / Biso min: 10.66 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→37.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|