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- PDB-4n08: Structure of Trypanosoma brucei brucei adenosine kinase (apo) -

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Basic information

Entry
Database: PDB / ID: 4n08
TitleStructure of Trypanosoma brucei brucei adenosine kinase (apo)
ComponentsAdenosine kinase
KeywordsTRANSFERASE / anion hole / adenosine kinase
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / glycosome / AMP salvage / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / nucleoplasm / ATP binding ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / glycosome / AMP salvage / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / 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 speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTimm, J. / Wilson, K.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structures of adenosine kinase from Trypanosoma brucei brucei.
Authors: Timm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 28, 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)38,2291
Polymers38,2291
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.084, 60.084, 192.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Adenosine kinase


Mass: 38228.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.6.2360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q584S0, adenosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M Tris, pH 8.8, 60% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→57.36 Å / Num. obs: 11649

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.8.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.292 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23082 551 4.8 %RANDOM
Rwork0.16705 ---
obs0.16999 10989 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.681 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 0 157 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192508
X-RAY DIFFRACTIONr_bond_other_d0.0010.022335
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9473406
X-RAY DIFFRACTIONr_angle_other_deg0.82235336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26923.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8281517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_mcbond_it2.5463.6541319
X-RAY DIFFRACTIONr_mcbond_other2.5453.6481318
X-RAY DIFFRACTIONr_mcangle_it3.8735.4681647
X-RAY DIFFRACTIONr_mcangle_other3.8725.4751648
X-RAY DIFFRACTIONr_scbond_it3.2563.8771189
X-RAY DIFFRACTIONr_scbond_other3.2553.8831190
X-RAY DIFFRACTIONr_scangle_other4.9965.7071759
X-RAY DIFFRACTIONr_long_range_B_refined6.69728.942867
X-RAY DIFFRACTIONr_long_range_B_other6.6428.8532829
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 42 -
Rwork0.141 789 -
obs--100 %

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