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- PDB-7p4q: Structure of the quinolinate synthase S124A variant complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p4q | ||||||
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Title | Structure of the quinolinate synthase S124A variant complexed with citrate | ||||||
![]() | Quinolinate synthase A | ||||||
![]() | TRANSFERASE / NAD biosynthesis / Iron Sulfur cluster / active site cavity | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Volbeda, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA. Authors: Basbous, H. / Volbeda, A. / Amara, P. / Rohac, R. / Martin, L. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.8 KB | Display | ![]() |
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PDB format | ![]() | 109.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p4mC ![]() 7p4pC ![]() 6i0pS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34640.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: nadA, TM_1644 Production host: ![]() ![]() References: UniProt: Q9X1X7, quinolinate synthase |
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-Non-polymers , 6 types, 296 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||
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#3: Chemical | ChemComp-FLC / | ||||
#4: Chemical | ChemComp-F3S / | ||||
#5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG4000, ammonium acetate, NaCl, trisodium citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→59.15 Å / Num. obs: 16403 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.351 / Num. unique obs: 1585 / CC1/2: 0.897 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6i0p Resolution: 2.2→59.15 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.58 Å2 / Biso mean: 34.9661 Å2 / Biso min: 14.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→59.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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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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