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- PDB-7owh: Odinarchaeota Adenylate kinase (OdinAK) native structure -

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Basic information

Entry
Database: PDB / ID: 7owh
TitleOdinarchaeota Adenylate kinase (OdinAK) native structure
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group
Function / homologyAAA domain / adenylate kinase / AMP kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / Adenylate kinase
Function and homology information
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

Downloads & links

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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)137,58514
Polymers137,3016
Non-polymers2848
Water8,449469
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7576
Polymers68,6513
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-76 kcal/mol
Surface area28190 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8288
Polymers68,6513
Non-polymers1775
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-90 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.761, 77.772, 217.611
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Bis-Tris Propane pH 7.0, 0.1 M, PEG 3350 12%, CuCl2 83 microM. Protein stored in 0.030 M MOPS, 0.05 M NaCl, pH 6.8

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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: 1.85→49.08 Å / Num. obs: 113276 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 2.028 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11096 / CC1/2: 0.646 / Rpim(I) all: 0.813

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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: 1.85→49.08 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 5808 5.13 %
Rwork0.1949 107468 -
obs0.1974 113276 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.26 Å2 / Biso mean: 45.7032 Å2 / Biso min: 18.02 Å2
Refinement stepCycle: final / Resolution: 1.85→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9467 0 8 475 9950
Biso mean--56.56 42.36 -
Num. residues----1168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.870.37751740.317635193693
1.87-1.890.331960.299935373733
1.89-1.920.35491780.270134923670
1.92-1.940.29882290.265435603789
1.94-1.970.32911840.257635563740
1.97-1.990.29771990.256835673766
1.99-2.020.31311970.250934923689
2.02-2.050.31252090.235835543763
2.05-2.080.27541940.225735273721
2.08-2.120.26961730.219935793752
2.12-2.150.28581880.221435593747
2.15-2.190.23442070.205435273734
2.19-2.240.26321870.200935653752
2.24-2.280.26762150.195235423757
2.28-2.330.27491620.20535543716
2.33-2.390.22811810.20435973778
2.39-2.440.25961940.200435803774
2.44-2.510.27731740.208735933767
2.51-2.580.29242350.217735123747
2.58-2.670.29672100.217535663776
2.67-2.760.25511760.209335853761
2.76-2.870.28181770.211236273804
2.87-30.2531710.206836073778
3-3.160.25711970.220535963793
3.16-3.360.23332170.211135783795
3.36-3.620.22931800.190636403820
3.62-3.980.22242220.168935953817
3.99-4.560.1831740.140937083882
4.56-5.750.19211680.148737103878
5.75-49.080.2262400.186838444084

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