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- PDB-5ktm: Crystal structure of Pyrococcus horikoshii quinolinate synthase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ktm | ||||||||||||
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Title | Crystal structure of Pyrococcus horikoshii quinolinate synthase (NadA) with a bound Fe4S4 cluster | ||||||||||||
![]() | Quinolinate synthase A | ||||||||||||
![]() | TRANSFERASE / Dehydratase / iron-sulfur cluster / holoenzyme / 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 | ![]() | 142.8 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ktnSC ![]() 5ktoC ![]() 5ktpC ![]() 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
#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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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % / 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. PH range: 5.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 43765 / % possible obs: 93.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/av σ(I): 29.8 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.44→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4.4 / % possible all: 83.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KTN Resolution: 1.44→42.221 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→42.221 Å
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Refine LS restraints |
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LS refinement shell |
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