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Yorodumi- PDB-4wio: Crystal structure of the C89A GMP synthetase inactive mutant from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wio | ||||||
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Title | Crystal structure of the C89A GMP synthetase inactive mutant from Plasmodium falciparum in complex with glutamine | ||||||
Components | GMP synthetaseGMP synthase | ||||||
Keywords | LIGASE / GMP synthetase / purine salvage pathway | ||||||
Function / homology | Function and homology information Purine ribonucleoside monophosphate biosynthesis / Azathioprine ADME / GMP synthase activity / GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / GMP biosynthetic process / purine nucleotide biosynthetic process / glutamine metabolic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Ballut, L. / Violot, S. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation. Authors: Ballut, L. / Violot, S. / Shivakumaraswamy, S. / Thota, L.P. / Sathya, M. / Kunala, J. / Dijkstra, B.W. / Terreux, R. / Haser, R. / Balaram, H. / Aghajari, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wio.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wio.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/4wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/4wio | HTTPS FTP |
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-Related structure data
Related structure data | 4wimC 4winC 3uowS C: citing same article (ref.) S: Starting model for refinement |
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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: 65312.367 Da / Num. of mol.: 1 / Fragment: UNP residues 2-555 / Mutation: C89A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: PF10_0123 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) References: UniProt: Q8IJR9, GMP synthase (glutamine-hydrolysing) |
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#2: Chemical | ChemComp-GLN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 22.5% (w/v) PEG 1000 and 10 mM Gln |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07812 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07812 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→61.5 Å / Num. obs: 11311 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3.47→3.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.92 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UOW Resolution: 3.15→48.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 35.74 / 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: 3.15→48.03 Å
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Refine LS restraints |
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LS refinement shell |
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