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- PDB-4o1g: MTB adenosine kinase in complex with gamma-Thio-ATP -

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Basic information

Entry
Database: PDB / ID: 4o1g
TitleMTB adenosine kinase in complex with gamma-Thio-ATP
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Adenosine Kinase
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDostal, J. / Brynda, J. / Hocek, M. / Pichova, I.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Basis for Inhibition of Mycobacterial and Human Adenosine Kinase by 7-Substituted 7-(Het)aryl-7-deazaadenine Ribonucleosides
Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, ...Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, P. / Votruba, I. / Hajduch, M. / Rezacova, P. / Veverka, V. / Hocek, M. / Pichova, I.
History
DepositionDec 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,0503
Polymers34,5041
Non-polymers5462
Water2,522140
1
A: Adenosine kinase
hetero molecules

A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1006
Polymers69,0082
Non-polymers1,0924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area4560 Å2
ΔGint-33 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.843, 72.410, 82.430
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

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Components

#1: Protein Adenosine kinase / / AK


Mass: 34503.953 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.34 Å3/Da / Density % sol: 47.43 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.49→40.66 Å / Num. obs: 51801 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.672 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 21.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.49-1.580.740.6062.2632870843283210.70198.7
1.58-1.690.9050.3344.0131281787278360.38699.5
1.69-1.820.9690.1857.2329192731672980.21399.8
1.82-20.9940.08514.6726992674167280.09899.8
2-2.230.9980.04426.4924357607860750.051100
2.23-2.580.9990.03136.4621755544354290.03699.7
2.58-3.150.9990.02547.418019456645570.02899.8
3.15-4.450.9990.0258.214144356335590.02399.9
4.450.9980.02159.587640201819980.02599

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.677 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2537 5 %RANDOM
Rwork0.1856 ---
obs0.1868 50733 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.15 Å2 / Biso mean: 26.3218 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.21 Å2
2--0.27 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 32 140 2569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192495
X-RAY DIFFRACTIONr_bond_other_d0.0010.021593
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.973407
X-RAY DIFFRACTIONr_angle_other_deg0.93333891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09824.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 183 -
Rwork0.249 3429 -
all-3612 -
obs--99.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4474-0.10450.05020.0638-0.17530.83230.01590.1847-0.0601-0.0628-0.0050.01350.2184-0.1126-0.01090.1025-0.0533-0.0080.1133-0.02660.0193-19.1910.656-30.715
21.91580.0638-0.80760.1613-0.19770.96560.0667-0.03590.1889-0.02690.01640.00930.0561-0.0182-0.08310.0257-0.0180.00320.01510.0020.0664-16.2755.106-9.127
32.3880.04530.08440.1641-0.13811.0436-0.1050.1856-0.3556-0.05340.0059-0.05450.17440.06490.09910.0740.01330.04570.0256-0.02260.0913-0.505-5.246-16.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 140
2X-RAY DIFFRACTION2A141 - 254
3X-RAY DIFFRACTION3A255 - 323

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