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- PDB-7owl: Odinarchaeota Adenylate kinase (OdinAK) in complex with CTP -

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Basic information

Entry
Database: PDB / ID: 7owl
TitleOdinarchaeota Adenylate kinase (OdinAK) in complex with CTP
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group / CTP
Function / homologyAAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / CYTIDINE-5'-TRIPHOSPHATE / Adenylate kinase
Function and homology information
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,20012
Polymers137,3016
Non-polymers2,8996
Water48627
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1006
Polymers68,6513
Non-polymers1,4493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-45 kcal/mol
Surface area27130 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1006
Polymers68,6513
Non-polymers1,4493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-51 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.486, 77.631, 216.881
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.) Candidatus Odinarchaeota archaeon LCB_4 (archaea)
Gene: adkA_1, OdinLCB4_00710 / Variant: Odinarchaeaota / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9I8, adenylate kinase
#2: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein buffer: 0.030 M MOPS, 0.050 M NaCl pH 7.0. Crystallization: Bis-Tris Propane pH 7.0, 0.1 M, PEG 3350 12-18% Odin 0.678 milliM, CTP 6.37 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 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→15.01 Å / Num. obs: 29184 / % possible obs: 99.3 % / Redundancy: 8.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.315 / Rpim(I) all: 0.163 / Net I/σ(I): 5.5
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 1.732 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2878 / CC1/2: 0.628 / Rpim(I) all: 0.904 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7owe

7owe


Resolution: 2.9→15.01 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1374 4.71 %
Rwork0.1918 27810 -
obs0.1947 29184 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 298.38 Å2 / Biso mean: 67.2273 Å2 / Biso min: 21.74 Å2
Refinement stepCycle: final / Resolution: 2.9→15.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9329 0 174 27 9530
Biso mean--93.46 46.71 -
Num. residues----1151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-30.35151440.260127342878
3-3.120.31531100.261527612871
3.12-3.260.31551500.247827142864
3.26-3.430.32121260.235627672893
3.43-3.650.27061330.217427752908
3.65-3.920.29191590.195927192878
3.92-4.310.22551400.16327832923
4.31-4.910.20751460.159327892935
4.91-6.120.22951390.187428192958
6.12-15.010.22241270.16729493076

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