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- PDB-2pkf: Crystal structure of M tuberculosis Adenosine Kinase (apo) -

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Basic information

Entry
Database: PDB / ID: 2pkf
TitleCrystal structure of M tuberculosis Adenosine Kinase (apo)
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / adenosine kinase / 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 / phosphorylation / 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
Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
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
B: Adenosine kinase


Theoretical massNumber of molelcules
Total (without water)71,3662
Polymers71,3662
Non-polymers00
Water19,9251106
1
A: Adenosine kinase

A: Adenosine kinase


Theoretical massNumber of molelcules
Total (without water)71,3662
Polymers71,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3110 Å2
ΔGint-19 kcal/mol
Surface area27580 Å2
MethodPISA, PQS
2
B: Adenosine kinase


Theoretical massNumber of molelcules
Total (without water)35,6831
Polymers35,6831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Adenosine kinase

B: Adenosine kinase


Theoretical massNumber of molelcules
Total (without water)71,3662
Polymers71,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)114.272, 75.184, 94.730
Angle α, β, γ (deg.)90.00, 121.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 324 / Label seq-ID: 12 - 334

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Adenosine kinase /


Mass: 35683.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2202 / Production host: Escherichia coli (E. coli)
References: UniProt: P83734, UniProt: P9WID5*PLUS, adenosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 100 mM sodium cacodylate pH 6.5, and 200 mM magnesium acetate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2005
RadiationMonochromator: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→81.11 Å / Num. all: 104080 / Num. obs: 104080 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.5→1.53 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceGUI interface - Modified in 23IDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-met MAD low resolution structure

Resolution: 1.5→81.11 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.184 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19831 5485 5 %RANDOM
Rwork0.17497 ---
obs0.17615 104080 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.532 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.91 Å2
2---0.11 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→81.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4989 0 0 1106 6095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9516920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82123.982221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34715791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7971532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22441
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23543
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2840
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.2123
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.881.53348
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17425212
X-RAY DIFFRACTIONr_scbond_it2.06531955
X-RAY DIFFRACTIONr_scangle_it3.1964.51708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2412 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.620.5
medium thermal0.892
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 399 -
Rwork0.194 7677 -
obs--99.99 %

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