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- PDB-5f3d: Structure of quinolinate synthase in complex with reaction interm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f3d | |||||||||
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Title | Structure of quinolinate synthase in complex with reaction intermediate W | |||||||||
![]() | Quinolinate synthase A | |||||||||
![]() | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | |||||||||
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. / Fontecilla-Camps, J.C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() Title: STRUCTURE OF THE FE4S4 QUINOLINATE SYNTHASE NADA FROM THERMOTOGA MARITIMA 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.4 KB | Display | ![]() |
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PDB format | ![]() | 111.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5f33C ![]() 5f35C ![]() 5lqmC ![]() 5lqsC ![]() 4p3xS 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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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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SF4 / | ||
#3: Chemical | ChemComp-5UK / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG3350, Tris, LiSO4, NH4SO4, KCl, DHAP, oxaloacetic acid, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.2 Å / Num. obs: 23542 / % possible obs: 97 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.4 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4P3X Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.543 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / 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: 36.946 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45 Å
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Refine LS restraints |
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