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- PDB-7owe: Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a -

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Basic information

Entry
Database: PDB / ID: 7owe
TitleOdinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / AP5A
Function / homologyAAA domain / adenylate kinase / AMP kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Function and homology information
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGrundstrom, C. / Aberg-Zingmark, E. / 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
E: Adenylate kinase
F: Adenylate kinase
D: Adenylate kinase
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,79912
Polymers137,3016
Non-polymers5,4986
Water00
1
E: Adenylate kinase
F: Adenylate kinase
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4006
Polymers68,6513
Non-polymers2,7493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4006
Polymers68,6513
Non-polymers2,7493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.781, 143.164, 158.714
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-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Drop E7 PACT Screen: 0.2 M NaAc, 20% PEG 3550.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.75→71.6 Å / Num. obs: 42150 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Net I/σ(I): 9.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4139 / CC1/2: 0.626 / Rpim(I) all: 0.846 / % 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: 1ki9

1ki9


Resolution: 2.75→71.582 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 2232 5.3 %
Rwork0.226 39897 -
obs0.2285 42129 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.31 Å2 / Biso mean: 93.4972 Å2 / Biso min: 44.94 Å2
Refinement stepCycle: final / Resolution: 2.75→71.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9335 0 342 0 9677
Biso mean--97.41 --
Num. residues----1153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.75-2.80980.42621400.36272448
2.8098-2.87520.3521320.332433
2.8752-2.94710.34991260.31122485
2.9471-3.02680.38661230.3092482
3.0268-3.11580.35661640.30712441
3.1158-3.21640.37851180.29232457
3.2164-3.33140.33671460.2892481
3.3314-3.46470.29411340.272471
3.4647-3.62240.33041370.26472479
3.6224-3.81340.31791490.2452454
3.8134-4.05230.27641250.23152506
4.0523-4.36510.22561320.19852508
4.3651-4.80430.22391550.19682493
4.8043-5.49930.2331570.19332512
5.4993-6.92770.2561370.23142574
6.9277-71.580.25781570.1862673

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