+Open data
-Basic information
Entry | Database: PDB / ID: 1dgm | ||||||
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Title | CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII | ||||||
Components | ADENOSINE KINASE | ||||||
Keywords | TRANSFERASE / TOXOPLASMA GONDII / ADENOSINE KINASE / PURINE METABOLISM | ||||||
Function / homology | Function and homology information adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cook, W.J. / DeLucas, L.J. / Chattopadhyay, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Crystal structure of adenosine kinase from Toxoplasma gondii at 1.8 A resolution. Authors: Cook, W.J. / DeLucas, L.J. / Chattopadhyay, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dgm.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dgm.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dgm_validation.pdf.gz | 800.2 KB | Display | wwPDB validaton report |
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Full document | 1dgm_full_validation.pdf.gz | 804.6 KB | Display | |
Data in XML | 1dgm_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1dgm_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgm ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgm | HTTPS FTP |
-Related structure data
Related structure data | 1bx4S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38424.828 Da / Num. of mol.: 1 / Mutation: L179F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TVW2, adenosine kinase |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ADN / |
#5: Chemical | ChemComp-ACY / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: sodium sulfate, tris HCL, adenosine, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Recacha, R., (2000) Acta Crystallogr. Sect., D56, 76. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48 Å / Num. all: 317522 / Num. obs: 317522 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 89.3 |
Reflection | *PLUS Num. obs: 33069 / Num. measured all: 317522 |
Reflection shell | *PLUS % possible obs: 89.3 % / Rmerge(I) obs: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN ADENOSINE KINASE (PDB 1BX4) Resolution: 1.8→46.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1071084.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.04 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→46.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.293 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.273 / Rfactor obs: 0.273 |