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Open data
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Basic information
Entry | Database: PDB / ID: 5f35 | |||||||||
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Title | Structure of quinolinate synthase in complex with citrate | |||||||||
![]() | Quinolinate synthase A | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() 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: 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. / 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 | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 120.6 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 ![]() 5f3dC ![]() 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: 34656.598 Da / Num. of mol.: 1 / Mutation: K219R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SF4 / ![]() |
#3: Chemical | ChemComp-FLC / ![]() |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: PEG4000, Na3citrate, NH4acetate, NaCl, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.57→49.3 Å / Num. obs: 40043 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.57→1.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4P3X Resolution: 1.6→27.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.345 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.081 / 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: 20.114 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.77 Å
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Refine LS restraints |
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