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- PDB-2pkk: Crystal structure of M tuberculosis Adenosine Kinase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2pkk
TitleCrystal structure of M tuberculosis Adenosine Kinase complexed with 2-fluro adenosine
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / adenosine kinase / 2 fluro adenosine / Structural Genomics / TB Structural Genomics Consortium / TBSGC / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / dGTP binding / AMP salvage / purine ribonucleoside salvage / GTP binding / magnesium ion binding / ATP binding / plasma membrane
Similarity search - Function
: / pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2FA / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsReddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase: insights into the mechanism and specificity of this novel prokaryotic enzyme
Authors: Reddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)35,9682
Polymers35,6831
Non-polymers2851
Water4,360242
1
A: Adenosine kinase
hetero molecules

A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9374
Polymers71,3662
Non-polymers5702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area5610 Å2
ΔGint-17 kcal/mol
Surface area24630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.916, 71.916, 110.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-692-

HOH

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Components

#1: Protein Adenosine kinase


Mass: 35683.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK / Production host: Escherichia coli (E. coli)
References: UniProt: P83734, UniProt: P9WID5*PLUS, adenosine kinase
#2: Chemical ChemComp-2FA / 2-(6-AMINO-2-FLUORO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 2-FLUOROADENOSINE


Mass: 285.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12FN5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained in conditions containing 0.1 M HEPES-Na, pH 7.5 and 1.4 M trisodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 7, 2006
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 1.93→62.26 Å / Num. all: 23982 / Num. obs: 23982 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.19 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo MTB ADK

Resolution: 1.93→62.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.743 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 1289 5.1 %RANDOM
Rwork0.18908 ---
obs0.19165 23982 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→62.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 20 242 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212524
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9573435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84523.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9181516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021933
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21173
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21736
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.12451672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.05972579
X-RAY DIFFRACTIONr_scbond_it5.6449981
X-RAY DIFFRACTIONr_scangle_it7.5811856
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 83 -
Rwork0.22 1744 -
obs--99.19 %

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