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- PDB-1lii: STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND ... -

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Basic information

Entry
Database: PDB / ID: 1lii
TitleSTRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND AMP-PCP
Componentsadenosine kinase
KeywordsTRANSFERASE / ALPHA-BETA STRUCTURE
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / 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, small domain - #10 / Adenosine kinase / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE / Adenosine kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.73 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: 1DGY
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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2065
Polymers38,3741
Non-polymers8324
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.800, 47.100, 44.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


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

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Non-polymers , 5 types, 174 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 46.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5
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: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.72→10 Å / Num. obs: 38408 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.3
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.242 / % possible all: 98
Reflection
*PLUS
Highest resolution: 1.71 Å / Lowest resolution: 10 Å / % possible obs: 99 % / Num. measured all: 132352 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
EPMRphasing
TNTrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.73→10 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3400 10 %RANDOM
Rwork0.189 ---
obs0.189 34526 99 %-
all-35500 --
Refinement stepCycle: LAST / Resolution: 1.73→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 52 170 2659
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.178 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.178 / Highest resolution: 1.71 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.87

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