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Yorodumi- PDB-5byt: PRPP complexed with a single Mg in the active site of Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5byt | |||||||||
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Title | PRPP complexed with a single Mg in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD) | |||||||||
Components | Anthranilate phosphoribosyltransferase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PRPP / phosphoriboysl pyrophosphate / TB Structural Genomics Consortium / TBSGC / magnesium binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Evans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: To be Published Title: Binding and mimicking of the phosphate-rich substrate, PRPP. Authors: Evans, G.L. / Baker, E.N. / Lott, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5byt.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5byt.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 5byt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5byt_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5byt_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5byt_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 5byt_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byt ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byt | HTTPS FTP |
-Related structure data
Related structure data | 5bneC 5bo2C 5bo3C 5c1rC 3qr9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38948.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: trpD, Rv2192c, MTCY190.03c / Plasmid: pET23A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41(DE3)pLysS References: UniProt: P9WFX5, anthranilate phosphoribosyltransferase #2: Chemical | #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: Flat-diamond shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole-malate, 15% PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 49191 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QR9 CHAIN A Resolution: 2→39.29 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.34 / 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: 2→39.29 Å
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Refine LS restraints |
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LS refinement shell |
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