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- PDB-5noe: Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis -
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Open data
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Basic information
Entry | Database: PDB / ID: 5noe | ||||||
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Title | Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis | ||||||
![]() | Anthranilate phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / tryptophan biosynthesis / phosphoribosyltransferase / archaea / zinc binding | ||||||
Function / homology | ![]() anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perveen, S. / Rashid, N. / Papageorgiou, A.C. | ||||||
![]() | ![]() Title: Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure. Authors: Perveen, S. / Rashid, N. / Tang, X.F. / Imanaka, T. / Papageorgiou, A.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 | ![]() | 266.5 KB | Display | ![]() |
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PDB format | ![]() | 216.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.2 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 57.3 KB | Display | |
Data in CIF | ![]() | 84.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nofC ![]() 2gvqS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34381.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: HYPERTHERMOPHILE Source: (gene. exp.) ![]() ![]() Gene: trpD, TK0253 / Plasmid: TkTpD-pET21a / Details (production host): E.coli / Production host: ![]() ![]() References: UniProt: Q9YGB4, anthranilate phosphoribosyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % / Description: Rods |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% w/v PEG 3350, 0.2M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 10, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96598 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.91→49.27 Å / Num. obs: 100253 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2gvq Resolution: 1.91→49.27 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→49.27 Å
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Refine LS restraints |
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LS refinement shell |
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