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- PDB-4ube: CRYSTAL STRUCTURE OF M TUBERCULOSIS ADENOSINE KINASE COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 4ube
TitleCRYSTAL STRUCTURE OF M TUBERCULOSIS ADENOSINE KINASE COMPLEXED WITH 2-FLURO ADENOSINE
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Adenosine kinase / Complex / 2-Fluoroadenosine
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / AMP salvage / purine ribonucleoside salvage / ATP binding
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
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.933 Å
AuthorsReddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PO1 AI 68135 United States
Citation
Journal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF M TUBERCULOSIS ADENOSINE KINASE COMPLEXED WITH 2-FLURO ADENOSINE
Authors: Reddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C.
#1: Journal: 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
DepositionAug 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 4, 2019Group: Data collection / Category: reflns
Item: _reflns.B_iso_Wilson_estimate / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 area5640 Å2
ΔGint-17 kcal/mol
Surface area24490 Å2
MethodPISA
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-566-

HOH

21A-583-

HOH

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Components

#1: Protein Adenosine kinase / AK


Mass: 35683.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: adoK, cbhK, Mb2225c / Plasmid: pET28-b / Details (production host): N-terminal Histag / Production host: Escherichia coli (E. coli) / References: UniProt: P83736, 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

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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: 0.1 M HEPES-NA, PH 7.5 AND 1.4 M TRISODIUM CITRATE DIHYDRATE
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 120 K / Ambient temp details: 07-JUN-06
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2007
RadiationProtocol: 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 / Redundancy: 2 % / Rmerge(I) obs: 0.19 / Net I/av σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO MTB ADK

Resolution: 1.933→18.831 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 1289 5.1 %Random
Rwork0.1975 ---
obs0.1999 23982 99.78 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.832 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 34.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.0322 Å20 Å20 Å2
2--0.0322 Å20 Å2
3----0.0645 Å2
Refinement stepCycle: LAST / Resolution: 1.933→18.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 20 242 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082524
X-RAY DIFFRACTIONf_angle_d1.1023435
X-RAY DIFFRACTIONf_dihedral_angle_d14.356869
X-RAY DIFFRACTIONf_chiral_restr0.077392
X-RAY DIFFRACTIONf_plane_restr0.005449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)Rfactor Rfree error
1.933-2.01030.27721310.2275261499
2.0103-2.10170.28830.220.214226071000.34
2.1017-2.21240.27911600.220.20626181000.34
2.2124-2.35070.29021470.20772661100
2.3507-2.53190.29331150.21912645100
2.5319-2.78590.2621410.20442674100
2.7859-3.18740.26431550.21282656100
3.1874-4.00940.19861540.17762689100
4.0094-18.83170.21881390.187281299

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