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Yorodumi- PDB-5kny: Crystal structure of Mycobacterium tuberculosis hypoxanthine guan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kny | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with (3-((3R,4R)-3-(Guanin-9-yl)-4-((S)-2-hydroxy-2-phosphonoethoxy)pyrrolidin-1-yl)-3-oxopropyl)phosphonic acid | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/INHIBITOR / Phosphoribosyltransferase / Inhibitor / Complex / pyrrolidne nucleoside phosphonate / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information IMP biosynthetic process / guanine salvage / purine-containing compound salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / GMP biosynthetic process ...IMP biosynthetic process / guanine salvage / purine-containing compound salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / GMP biosynthetic process / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.91 Å | ||||||
Authors | Eng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate Authors: Eng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kny.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kny.ent.gz | 241.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/5kny ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5kny | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 22969.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: hpt, hprT, Rv3624c, MTCY15C10.28 / Production host: Escherichia coli (E. coli) References: UniProt: P9WHQ9, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-YPG / [ #3: Chemical | ChemComp-MG / #4: 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: 1.96 Å3/Da / Density % sol: 37.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Li2SO4, 0.1 M Sodium acetate pH 4.5 and 30% PEG8000 |
-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 270 / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→44.77 Å / Num. obs: 15646 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.91→3.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Resolution: 2.91→44.77 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.95 Å2 / Biso mean: 53.2634 Å2 / Biso min: 12.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.91→44.77 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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