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- PDB-1lik: STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE -

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Basic information

Entry
Database: PDB / ID: 1lik
TitleSTRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE
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
ADENOSINE / Adenosine kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsSchumacher, M.A. / Scott, D.M. / Mathews, I.I. / Ealick, S.E. / Roos, D.S. / Ullman, B. / 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
SupersessionMay 15, 2002ID: 1DH0
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0405
Polymers38,3741
Non-polymers6664
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.200, 47.010, 44.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein adenosine kinase /


Mass: 38373.824 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
25 mMadenosine1drop
31.1 M1reservoirLiSO4
410 mM1reservoirMgCl2
550 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→10 Å / Num. obs: 30369 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 10
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.109 / % possible all: 75
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. obs: 17172 / % possible obs: 97 % / Num. measured all: 30369 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
EPMRphasing
TNTrefinement
ADSCdata collection
RefinementResolution: 2.55→10 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1031 10 %RANDOM
Rwork0.15 ---
obs0.15 17172 99 %-
Refinement stepCycle: LAST / Resolution: 2.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 44 154 2631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.181
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 10 % / Rfactor obs: 0.13 / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.15

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