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- PDB-5ktp: Crystal structure of Pyrococcus horikoshii quinolinate synthase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ktp | ||||||||||||
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Title | Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with bound itaconate and Fe4S4 cluster | ||||||||||||
![]() | Quinolinate synthase A | ||||||||||||
![]() | TRANSFERASE / Dehydratase / iron-sulfur cluster / substrate analog complex / biosynthetic enzyme | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Fenwick, M.K. / Ealick, S.E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate. Authors: Fenwick, M.K. / Ealick, S.E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.5 KB | Display | ![]() |
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PDB format | ![]() | 107.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459 KB | Display | ![]() |
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Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ktmC ![]() 5ktnSC ![]() 5ktoC ![]() 5ktrC ![]() 5ktsC ![]() 5kttC C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34582.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: nadA, PH0013 / Plasmid: pDESTF1 Details (production host): Gateway-adapted vector based on the pET system (Novagen) Production host: ![]() ![]() |
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-Non-polymers , 5 types, 308 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ITN.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ITN.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ITN / |
#5: Chemical | ChemComp-NH4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.92 % / Description: Rod |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 210 mM ammonium chloride, 8 - 15% polyethylene glycol 4000, and 40 mM HEPES, pH 5.5 - 7.5. Itaconic acid, pH 6.0, was added to the cryopreservation solution to a final concentration of 7 mM PH range: 5.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→20 Å / Num. obs: 36334 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Net I/av σ(I): 23.8 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4.9 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KTN Resolution: 1.542→19.625 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.542→19.625 Å
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Refine LS restraints |
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LS refinement shell |
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