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- PDB-7owk: Odinarchaeota Adenylate kinase (OdinAK) in complex with dTTP -

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Basic information

Entry
Database: PDB / ID: 7owk
TitleOdinarchaeota Adenylate kinase (OdinAK) in complex with dTTP
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group / dTTP
Function / homologyAAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / THYMIDINE-5'-TRIPHOSPHATE / Adenylate kinase
Function and homology information
Biological speciesOdinarchaeota archaeon
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAberg-Zingmark, E. / Grundstrom, C. / Verma, A. / Wolf-Watz, M. / Sauer, U.H. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Sci Adv / Year: 2022
Title: Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.
Authors: Verma, A. / Aberg-Zingmark, E. / Sparrman, T. / Mushtaq, A.U. / Rogne, P. / Grundstrom, C. / Berntsson, R. / Sauer, U.H. / Backman, L. / Nam, K. / Sauer-Eriksson, E. / Wolf-Watz, M.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,19412
Polymers137,3016
Non-polymers2,8936
Water1086
1
B: Adenylate kinase
A: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0976
Polymers68,6513
Non-polymers1,4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-55 kcal/mol
Surface area27450 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0976
Polymers68,6513
Non-polymers1,4473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-51 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.824, 77.203, 214.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Adenylate kinase /


Mass: 22883.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odinarchaeota archaeon (strain LCB_4) (archaea)
Strain: LCB_4 / Gene: adkA_1, OdinLCB4_00710 / Variant: Odinarchaeaota / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9I8, adenylate kinase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 0.030 M MOPS, 0.050 M NaCl pH 7.0. Precipitant: Bis-Tris Propane pH 7.0, 0.1 M, PEG 3350 15-18% Odin 0.732 milliM, dTTP 5.8 milliM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→48.57 Å / Num. obs: 23925 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.356 / Net I/σ(I): 9.1
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 3.017 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2363 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OWE

7owe


Resolution: 3.1→48.567 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1196 5 %
Rwork0.206 22729 -
obs0.208 23925 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.78 Å2 / Biso mean: 70.3 Å2 / Biso min: 24 Å2
Refinement stepCycle: final / Resolution: 3.1→48.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9374 0 174 6 9554
Biso mean--73.32 44.58 -
Num. residues----1157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.22410.34631280.280824762604
3.2241-3.37080.36711310.258224712602
3.3708-3.54850.30861300.248324732603
3.5485-3.77070.31481320.220825112643
3.7707-4.06170.2581340.20325132647
4.0617-4.47020.22611300.180824912621
4.4702-5.11650.23071380.179325342672
5.1165-6.44380.2841360.225125742710
6.4438-48.5670.21791370.180426862823

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