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

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Basic information

Entry
Database: PDB / ID: 2pkn
TitleCrystal structure of M tuberculosis Adenosine Kinase complexed with AMP-PCP (non-hydrolyzable ATP analog)
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 18, 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

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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)36,1882
Polymers35,6831
Non-polymers5051
Water4,954275
1
A: Adenosine kinase
hetero molecules

A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3774
Polymers71,3662
Non-polymers1,0102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4700 Å2
ΔGint-25 kcal/mol
Surface area25550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.050, 75.184, 52.380
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-360-

HOH

31A-373-

HOH

41A-553-

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-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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
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: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 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: 1.9→57.54 Å / Num. all: 25991 / Num. obs: 25991 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo MTB ADK

Resolution: 1.9→57.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.016 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25781 1379 5 %RANDOM
Rwork0.20686 ---
obs0.2095 25991 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å2-1.11 Å2
2--1.04 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 31 275 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212478
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9673379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.08823.922102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87115375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.991515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021866
X-RAY DIFFRACTIONr_nbd_refined0.1850.21119
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3770.227
X-RAY DIFFRACTIONr_mcbond_it2.48651642
X-RAY DIFFRACTIONr_mcangle_it3.36772526
X-RAY DIFFRACTIONr_scbond_it4.3899965
X-RAY DIFFRACTIONr_scangle_it6.02411853
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 94 -
Rwork0.302 1940 -
obs--99.95 %

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