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- PDB-9r72: Crystal structure of Odinarchaeota Adenylate kinase (OdinAK) S74G... -

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Basic information

Entry
Database: PDB / ID: 9r72
TitleCrystal structure of Odinarchaeota Adenylate kinase (OdinAK) S74G mutant
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADENYLATE KINASE / ODINARCHAEOTA / S74G mutant / PHOSPHOTRANSFERASE
Function / homologyAAA domain / adenylate kinase / kinase activity / P-loop containing nucleoside triphosphate hydrolase / Adenylate kinase
Function and homology information
Biological speciesCandidatus Odinarchaeum yellowstonii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsRodriguez Buitrago, J.A. / Schierholz, L. / Mattsson, J. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase
Authors: Mattsson, J. / Phoeurk, C. / Schierholz, L. / Mushtaq, A.U. / Rodriguez Buitrago, J.A. / Rogne, P. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,29811
Polymers137,1216
Non-polymers1775
Water362
1
B: Adenylate kinase
C: Adenylate kinase
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6676
Polymers68,5603
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-64 kcal/mol
Surface area27340 Å2
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6315
Polymers68,5603
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-74 kcal/mol
Surface area27840 Å2
Unit cell
Length a, b, c (Å)77.635, 77.004, 115.857
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenylate kinase


Mass: 22853.490 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Odinarchaeum yellowstonii (archaea)
Gene: OdinLCB4_000095 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAF0D2B2, adenylate kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.58→43.66 Å / Num. obs: 16240 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.963 / Rmerge(I) obs: 0.512 / Rpim(I) all: 0.23 / Net I/σ(I): 3.3
Reflection shellResolution: 3.58→3.71 Å / Rmerge(I) obs: 2.151 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1615 / CC1/2: 0.374 / Rpim(I) all: 1.055 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→43.66 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 809 4.99 %
Rwork0.2436 --
obs0.2453 16212 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.58→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9282 0 5 2 9289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069463
X-RAY DIFFRACTIONf_angle_d0.87112803
X-RAY DIFFRACTIONf_dihedral_angle_d20.8373617
X-RAY DIFFRACTIONf_chiral_restr0.0491465
X-RAY DIFFRACTIONf_plane_restr0.0061638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.80.37681340.35882554X-RAY DIFFRACTION100
3.8-4.10.31051350.2982547X-RAY DIFFRACTION100
4.1-4.510.25541340.24992549X-RAY DIFFRACTION100
4.51-5.160.26311350.22642564X-RAY DIFFRACTION100
5.16-6.50.3231350.26062570X-RAY DIFFRACTION100
6.5-43.660.23061360.18822619X-RAY DIFFRACTION99

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