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Yorodumi- PDB-5bxi: 1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5bxi | ||||||
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| Title | 1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii with Tyrosine of Tag Bound to Active Site | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 2-Layer Sandwich / Putative Nucleoside Diphosphate Kinase | ||||||
| Function / homology | Function and homology informationnucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Minasov, G. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Front Cell Infect Microbiol / Year: 2018Title: CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii . Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. ...Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. / Moulton, J.D. / Moulton, H. / McPhillie, M.J. / Muench, S.P. / Fishwick, C.W.G. / Sabini, E. / Shanmugam, D. / Roos, D.S. / McLeod, R. / Anderson, W.F. / Ngo, H.M. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5bxi.cif.gz | 792.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5bxi.ent.gz | 660.6 KB | Display | PDB format |
| PDBx/mmJSON format | 5bxi.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5bxi_validation.pdf.gz | 552 KB | Display | wwPDB validaton report |
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| Full document | 5bxi_full_validation.pdf.gz | 566.9 KB | Display | |
| Data in XML | 5bxi_validation.xml.gz | 86.5 KB | Display | |
| Data in CIF | 5bxi_validation.cif.gz | 126.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxi ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxi | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4nmlC ![]() 4nogC ![]() 4nu7C ![]() 4o0nSC ![]() 4odiC S: Starting model for refinement C: citing same article ( |
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| Similar structure data | |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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Components
| #1: Protein | Mass: 18238.816 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() Strain (production host): BL21(DE3)/pMagic References: UniProt: S8FF85, UniProt: B9Q287*PLUS, nucleoside-diphosphate kinase #2: Chemical | ChemComp-BCT / #3: Chemical | ChemComp-PEG / | #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: 2.2 Å3/Da / Density % sol: 44 % |
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| Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein:7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: PACT (B10), 0.2 M Magnesium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9789 Å |
| Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2015 |
| Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
| Reflection | Resolution: 1.7→30 Å / Num. all: 202729 / Num. obs: 202729 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 22 |
| Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 4O0N Resolution: 1.7→29.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.144 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 33.435 Å2
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| Refinement step | Cycle: 1 / Resolution: 1.7→29.98 Å
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