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- PDB-7owj: Odinarchaeota Adenylate kinase (OdinAK) in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 7owj
TitleOdinarchaeota Adenylate kinase (OdinAK) in complex with GTP
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group / GTP
Function / homologyAAA domain / adenylate kinase / AMP kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / GUANOSINE-5'-TRIPHOSPHATE / Adenylate kinase
Function and homology information
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)140,44012
Polymers137,3016
Non-polymers3,1396
Water2,738152
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2206
Polymers68,6513
Non-polymers1,5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-43 kcal/mol
Surface area27670 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2206
Polymers68,6513
Non-polymers1,5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-43 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.608, 78.787, 217.191
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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein in: 0.030 M MOPS, 0.050M NaCl, pH 6.8. Drop: 1:1 of Bis-Tris Propane pH 6.5 - 0.1 M, PEG 3350 12% Odin 0.853 mM, GTP 8.53 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→49.27 Å / Num. obs: 46830 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.088 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / Num. unique obs: 4562 / CC1/2: 0.708 / Rpim(I) all: 0.548 / % possible all: 98.5

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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: 2.5→49.27 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 2316 4.95 %
Rwork0.1868 44514 -
obs0.1904 46830 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 323.44 Å2 / Biso mean: 51.5686 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: final / Resolution: 2.5→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9446 0 192 153 9791
Biso mean--92.8 35.74 -
Num. residues----1165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.550.40051430.3122494263797
2.55-2.610.34681430.269125822725100
2.61-2.670.36741260.24612564269099
2.67-2.730.29361150.226826172732100
2.73-2.810.31041400.235825892729100
2.81-2.890.31221550.228425792734100
2.89-2.980.29821200.223526122732100
2.98-3.090.28071240.231825922716100
3.09-3.210.32681380.241325962734100
3.21-3.360.32481110.212126342745100
3.36-3.540.24591290.196826172746100
3.54-3.760.26571390.179326092748100
3.76-4.050.21861450.154126262771100
4.05-4.460.2121280.13126642792100
4.46-5.10.20271420.13326422784100
5.1-6.420.25241480.1827052853100
6.43-49.270.2131700.165727922962100

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