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Yorodumi- PDB-5i33: Unligated adenylosuccinate synthetase from Cryptococcus neoformans -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i33 | ||||||
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Title | Unligated adenylosuccinate synthetase from Cryptococcus neoformans | ||||||
Components | Adenylosuccinate synthetaseAdenylosuccinate synthase | ||||||
Keywords | LIGASE / dimer / adenylosuccinate synthetase / purine metabolism | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptococcus neoformans var. grubii serotype A (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Blundell, R.D. / Williams, S.J. / Ericsson, D. / Fraser, J.A. / Kobe, B. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2016 Title: Disruption of de Novo Adenosine Triphosphate (ATP) Biosynthesis Abolishes Virulence in Cryptococcus neoformans. Authors: Blundell, R.D. / Williams, S.J. / Arras, S.D. / Chitty, J.L. / Blake, K.L. / Ericsson, D.J. / Tibrewal, N. / Rohr, J. / Koh, Y.Q. / Kappler, U. / Robertson, A.A. / Butler, M.S. / Cooper, M.A. ...Authors: Blundell, R.D. / Williams, S.J. / Arras, S.D. / Chitty, J.L. / Blake, K.L. / Ericsson, D.J. / Tibrewal, N. / Rohr, J. / Koh, Y.Q. / Kappler, U. / Robertson, A.A. / Butler, M.S. / Cooper, M.A. / Kobe, B. / Fraser, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i33.cif.gz | 304.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i33.ent.gz | 249 KB | Display | PDB format |
PDBx/mmJSON format | 5i33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/5i33 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/5i33 | HTTPS FTP |
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-Related structure data
Related structure data | 5i34C 1j4bS 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: 47939.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus) Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02858 / Plasmid: PQE30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J9VI09, adenylosuccinate synthase #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: 2.58 Å3/Da / Density % sol: 52.25 % Description: Long rectangular crystals, approximately 0.5 by 0.05 by 0.05 mm |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M bis-tris propane pH 8 0.2 M sodium bromide 17% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.02 Å / Num. obs: 49839 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.8 |
Reflection shell | Highest resolution: 2.2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J4B Resolution: 2.2→37.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.02 Å
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Refine LS restraints |
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LS refinement shell |
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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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