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- PDB-1lio: STRUCTURE OF APO T. GONDII ADENOSINE KINASE -

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Basic information

Entry
Database: PDB / ID: 1lio
TitleSTRUCTURE OF APO T. GONDII ADENOSINE KINASE
Componentsadenosine kinase
KeywordsTRANSFERASE / ALPHA-BETA STRUCTURE
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSchumacher, M.A. / Scott, D.M. / Mathews, I.I. / Ealick, S.E. / Brennan, R.G.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding.
Authors: Schumacher, M.A. / Scott, D.M. / Mathews, I.I. / Ealick, S.E. / Roos, D.S. / Ullman, B. / Brennan, R.G.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2002ID: 1DH2
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adenosine kinase


Theoretical massNumber of molelcules
Total (without water)38,3651
Polymers38,3651
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 68.000, 56.800
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein adenosine kinase / / AK / Adenosine 5'-phosphotransferase


Mass: 38364.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: PBACE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TVW2, adenosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 28789 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.23 / % possible all: 85

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Processing

Software
NameClassification
MERLOTphasing
TNTrefinement
bioteXdata reduction
bioteXdata scaling
RefinementResolution: 2.5→10 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1000 -RANDOM
Rwork0.198 ---
obs0.2 12000 99 %-
all-12312 --
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 179 2599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.903

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