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- PDB-6f7u: Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase -

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Basic information

Entry
Database: PDB / ID: 6f7u
TitleMolecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate Kinase / ATP selectivity / GTP inhibition / inhibitor complex
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRogne, P. / Rosselin, M. / Grundstrom, C. / Hedberg, C. / Wolf-Watz, M. / Sauer, U.H.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2013.0187 Sweden
Swedish Research Council Sweden
Kempe Foundation Sweden
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Molecular mechanism of ATP versus GTP selectivity of adenylate kinase.
Authors: Rogne, P. / Rosselin, M. / Grundstrom, C. / Hedberg, C. / Sauer, U.H. / Wolf-Watz, M.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 25, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref / struct_ref_seq
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.1May 1, 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: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1663
Polymers23,6201
Non-polymers5462
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.880, 31.779, 54.205
Angle α, β, γ (deg.)90.00, 112.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-613-

HOH

31A-638-

HOH

41A-673-

HOH

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 23620.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69441, adenylate kinase
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 8000, 0.2 M Na-Acetate, 0.1 M Na-Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.4→33.1 Å / Num. obs: 89469 / % possible obs: 96.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.036 / Rrim(I) all: 0.059 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 5638 / CC1/2: 0.71 / Rpim(I) all: 0.63 / Rrim(I) all: 1.13 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AKE_A

Resolution: 1.4→33.1 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.47
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 915 2.23 %Random selection
Rwork0.175 ---
obs0.1754 41048 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 33 306 1995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091820
X-RAY DIFFRACTIONf_angle_d1.0832469
X-RAY DIFFRACTIONf_dihedral_angle_d19.054720
X-RAY DIFFRACTIONf_chiral_restr0.074271
X-RAY DIFFRACTIONf_plane_restr0.006324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.47380.2251290.19815638X-RAY DIFFRACTION98
1.4738-1.56610.19411340.19295661X-RAY DIFFRACTION98
1.5661-1.68710.20391260.18245638X-RAY DIFFRACTION97
1.6871-1.85680.18471350.18485754X-RAY DIFFRACTION99
1.8568-2.12550.22591300.17815751X-RAY DIFFRACTION99
2.1255-2.67770.17041270.17385770X-RAY DIFFRACTION98
2.6777-33.16780.18381340.16655921X-RAY DIFFRACTION99

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