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- PDB-6c67: Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin -

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Basic information

Entry
Database: PDB / ID: 6c67
TitleMycobacterium tuberculosis adenosine kinase bound to iodotubercidin
ComponentsAdenosine kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Nucleoside analog / Complex / Inhibitor / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-5ID / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCrespo, R.A. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1024055 United States
Welch FoundationA-0015 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase.
Authors: Crespo, R.A. / Dang, Q. / Zhou, N.E. / Guthrie, L.M. / Snavely, T.C. / Dong, W. / Loesch, K.A. / Suzuki, T. / You, L. / Wang, W. / O'Malley, T. / Parish, T. / Olsen, D.B. / Sacchettini, J.C.
History
DepositionJan 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,90711
Polymers69,0082
Non-polymers1,8999
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA, Sedimentation experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-58 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.056, 49.056, 262.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenosine kinase / AK


Mass: 34503.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: adoK, cbhK, Rv2202c, MTCY190.13c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WID5, adenosine kinase

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Non-polymers , 5 types, 268 molecules

#2: Chemical
ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13IN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 2.0 M ammonium sulfate, 2.0% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.105→34.69 Å / Num. obs: 34540 / % possible obs: 96.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 40.73 Å2 / Rmerge(I) obs: 0.0793 / Net I/σ(I): 23.36
Reflection shellResolution: 2.11→2.18 Å / Rmerge(I) obs: 0.2468 / Num. unique obs: 3485 / CC1/2: 0.985 / Rpim(I) all: 0.09564 / Rrim(I) all: 0.2648

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PKM

2pkm


Resolution: 2.11→34.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1649 4.8 %
Rwork0.194 --
obs0.196 34380 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 98 259 5033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034861
X-RAY DIFFRACTIONf_angle_d0.5976620
X-RAY DIFFRACTIONf_dihedral_angle_d15.4872811
X-RAY DIFFRACTIONf_chiral_restr0.043766
X-RAY DIFFRACTIONf_plane_restr0.004849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.105-2.1670.29231570.23462745X-RAY DIFFRACTION98
2.167-2.23690.321370.22172826X-RAY DIFFRACTION99
2.2369-2.31680.23291360.21912763X-RAY DIFFRACTION99
2.3168-2.40960.20841300.20972775X-RAY DIFFRACTION99
2.4096-2.51920.24711720.21482736X-RAY DIFFRACTION99
2.5192-2.6520.28011450.19322812X-RAY DIFFRACTION99
2.652-2.8180.23821240.20052820X-RAY DIFFRACTION99
2.818-3.03550.22461120.21492836X-RAY DIFFRACTION99
3.0355-3.34080.29171340.21442713X-RAY DIFFRACTION96
3.3408-3.82360.2051970.17852593X-RAY DIFFRACTION90
3.8236-4.81530.17641580.16232489X-RAY DIFFRACTION89
4.8153-34.69250.24681470.19292623X-RAY DIFFRACTION93

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