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- PDB-1lij: STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO PRODRUG 2 7-IODO... -

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Basic information

Entry
Database: PDB / ID: 1lij
TitleSTRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO PRODRUG 2 7-IODOTUBERCIDIN 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 / nucleus / metal ion binding / cytosol
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-RPP / Adenosine kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 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: 1DH1
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)39,3345
Polymers38,3741
Non-polymers9604
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.700, 46.970, 44.090
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, 149 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-RPP / 2-RIBOFURANOSYL-3-IODO-2,3-DIHYDRO-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 395.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14IN5O4
#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.: 145 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.54181
ReflectionResolution: 1.7→10 Å / Num. obs: 35168 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 5
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.244 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 1.84 Å / Lowest resolution: 10 Å / Num. obs: 32045 / % possible obs: 97 % / Num. measured all: 124975 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
EPMRphasing
TNTrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.86→10 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2956 10 %RANDOM
Rwork0.185 ---
obs0.185 32045 99 %-
Refinement stepCycle: LAST / Resolution: 1.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 53 145 2631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.947
Refinement
*PLUS
Highest resolution: 1.84 Å / % reflection Rfree: 10 % / Rfactor obs: 0.181 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.99

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