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Yorodumi- PDB-5noe: Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5noe | ||||||
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Title | Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / tryptophan biosynthesis / phosphoribosyltransferase / archaea / zinc binding | ||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Perveen, S. / Rashid, N. / Papageorgiou, A.C. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5noe.cif.gz | 266.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5noe.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 5noe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5noe ftp://data.pdbj.org/pub/pdb/validation_reports/no/5noe | HTTPS FTP |
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-Related structure data
Related structure data | 5nofC 2gvqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Gene: trpD, TK0253 / Plasmid: TkTpD-pET21a / Details (production host): E.coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL References: UniProt: Q9YGB4, anthranilate phosphoribosyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96598 Å | |||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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