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- PDB-2xtb: Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kin... -

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Basic information

Entry
Database: PDB / ID: 2xtb
TitleCrystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with Activator
ComponentsADENOSINE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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
4-[5-(4-PHENOXYPHENYL)-1H-PYRAZOL-3-YL]MORPHOLINE / Adenosine kinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI RHODESIENSE (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R.
CitationJournal: Plos Negl Trop Dis / Year: 2011
Title: Crystal Structures of T. B. Rhodesiense Adenosine Kinase Complexed with Inhibitor and Activator: Implications for Catalysis and Hyperactivation.
Authors: Kuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R.
History
DepositionOct 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ADENOSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4532
Polymers38,1311
Non-polymers3211
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 61.240, 193.850
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: 38131.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI RHODESIENSE (eukaryote)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q584S0, adenosine kinase
#2: Chemical ChemComp-KRM / 4-[5-(4-PHENOXYPHENYL)-1H-PYRAZOL-3-YL]MORPHOLINE


Mass: 321.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST TWO RESIDUES ARE RESULT OF THROMBIN CLEAVAGE OF AFFINITY TAG. THE ALA IN POSITION TWO IS ...THE FIRST TWO RESIDUES ARE RESULT OF THROMBIN CLEAVAGE OF AFFINITY TAG. THE ALA IN POSITION TWO IS A CLONING ARTIFACT.

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→58 Å / Num. obs: 9747 / % possible obs: 98 % / Observed criterion σ(I): -10 / Redundancy: 3.2 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→58.42 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.824 / SU B: 18.003 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29646 441 4.7 %RANDOM
Rwork0.23158 ---
obs0.23453 9034 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 24 24 2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.9623613
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8065335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62923.613119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3321520
X-RAY DIFFRACTIONr_chiral_restr0.060.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022023
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.21266
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21834
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2761.51710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49622681
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.45631076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7894.5932
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 34 -
Rwork0.308 635 -
obs--97.38 %

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