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- PDB-8rj4: E. coli adenylate kinase in complex with two ADP molecules and Mg... -

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Basic information

Entry
Database: PDB / ID: 8rj4
TitleE. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ATP:AMP PHOSPHOTRANSFERASE / ENERGY METABOLISM / AP4A HYDROLYSIS / POTENTIAL MOONLIGHTING PROTEIN
Function / homology
Function and homology information


purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding ...purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTischlik, S. / Ronge, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Sci Adv / Year: 2024
Title: Magnesium induced structural reorganization in the active site of adenylate kinase.
Authors: Nam, K. / Thodika, A.R.A. / Tischlik, S. / Phoeurk, C. / Nagy, T.M. / Schierholz, L. / Aden, J. / Rogne, P. / Drescher, M. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
#1: Journal: Biochemistry / Year: 2023
Title: Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by
Authors: Tischlik, S. / Oelker, M. / Rogne, P. / Sauer-Eriksson, A.E. / Drescher, M. / Wolf-Watz, M.
History
DepositionDec 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,01716
Polymers94,4804
Non-polymers3,53712
Water8,503472
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4994
Polymers23,6201
Non-polymers8793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4994
Polymers23,6201
Non-polymers8793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5104
Polymers23,6201
Non-polymers8903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5104
Polymers23,6201
Non-polymers8903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.385, 76.290, 93.391
Angle α, β, γ (deg.)90.00, 110.76, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→44.71 Å / Num. obs: 55145 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.083 / Net I/σ(I): 8.5
Reflection shellResolution: 2.11→2.19 Å / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5433 / CC1/2: 0.668 / Rpim(I) all: 0.903

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→44.71 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 2843 5.16 %
Rwork0.191 --
obs0.194 55092 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.36 Å2
Refinement stepCycle: LAST / Resolution: 2.11→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 220 472 7316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.140.37911490.32342455X-RAY DIFFRACTION94
2.14-2.180.37061530.29882596X-RAY DIFFRACTION99
2.18-2.230.34881370.27042605X-RAY DIFFRACTION99
2.23-2.270.34121360.25032578X-RAY DIFFRACTION99
2.27-2.320.32461400.23572602X-RAY DIFFRACTION99
2.32-2.370.32031320.23622623X-RAY DIFFRACTION99
2.37-2.430.31561450.22012585X-RAY DIFFRACTION99
2.43-2.50.25551420.21132609X-RAY DIFFRACTION99
2.5-2.570.33071450.20762622X-RAY DIFFRACTION99
2.57-2.660.30831300.20812611X-RAY DIFFRACTION99
2.66-2.750.29771300.20922641X-RAY DIFFRACTION99
2.75-2.860.2961650.21062598X-RAY DIFFRACTION99
2.86-2.990.29151250.20752627X-RAY DIFFRACTION99
2.99-3.150.25031330.22628X-RAY DIFFRACTION99
3.15-3.350.24091430.192638X-RAY DIFFRACTION99
3.35-3.60.23491400.18622634X-RAY DIFFRACTION99
3.6-3.970.23791500.16242608X-RAY DIFFRACTION99
3.97-4.540.1871650.15382627X-RAY DIFFRACTION99
4.54-5.720.21861190.1572697X-RAY DIFFRACTION100
5.72-44.710.21531640.16792665X-RAY DIFFRACTION98

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