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- PDB-2a9z: Crystal structure of T. gondii adenosine kinase complexed with N6... -

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Basic information

Entry
Database: PDB / ID: 2a9z
TitleCrystal structure of T. gondii adenosine kinase complexed with N6-dimethyladenosine and AMP-PCP
Componentsadenosine kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / ribokinase fold / alpha/beta / intermediate conformation
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
6N-DIMETHYLADENOSINE / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Adenosine kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsZhang, Y. / el Kouni, M.H. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase
Authors: Zhang, Y. / El Kouni, M.H. / Ealick, S.E.
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)41,7617
Polymers40,5841
Non-polymers1,1776
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.068, 61.588, 91.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein adenosine kinase / / E.C.2.7.1.20 / AK / Adenosine 5'-phosphotransferase


Mass: 40584.105 Da / Num. of mol.: 1 / Mutation: G270S, S360F, L361T, P362S, C363G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9TVW2, adenosine kinase

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Non-polymers , 5 types, 388 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-26A / 6N-DIMETHYLADENOSINE


Mass: 295.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N5O4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.1 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, ammonium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2004
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 74024 / Num. obs: 74024 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.044 / Net I/σ(I): 35.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 6405 / Rsym value: 0.303 / % possible all: 86

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LIO

1lio


Resolution: 1.35→10 Å / Num. parameters: 28048 / Num. restraintsaints: 34952 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 5332 8.3 %RANDOM
Rwork0.1371 ---
all0.1411 64552 --
obs0.1411 64552 86 %-
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3033
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 76 382 3116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0266
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.095
LS refinement shellResolution: 1.35→1.41 Å /
RfactorNum. reflection
Rwork0.202 -
obs-6654

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