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- PDB-9iac: Structure of the Argonaute-associated Cas4 family protein 1 (ACE1... -

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Basic information

Entry
Database: PDB / ID: 9iac
TitleStructure of the Argonaute-associated Cas4 family protein 1 (ACE1) from Microcystis aeruginosa (MaACE1)
ComponentsSimilar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein
KeywordsIMMUNE SYSTEM / Cas4 family protein / deoxyribonuclease / hydrolase
Function / homologyPD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / PD-(D/E)XK endonuclease-like domain superfamily / IRON/SULFUR CLUSTER / Similar to tr
Function and homology information
Biological speciesMicrocystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsBobadilla Ugarte, P. / Halter, S. / Jinek, M. / Swarts, D.C.
Funding supportEuropean Union, Netherlands, Mexico, 5items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2020-STG 948783European Union
Netherlands Organisation for Scientific Research (NWO)016.Veni.192.072 Netherlands
Consejo Nacional de Ciencia y Tecnologia (CONACYT)682509 Mexico
European Molecular Biology Organization (EMBO)ALTF 179-2015European Union
European Molecular Biology Organization (EMBO)aALTF 509-2017European Union
CitationJournal: Mol.Cell / Year: 2025
Title: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.
Authors: Bobadilla Ugarte, P. / Halter, S. / Mutte, S.K. / Heijstek, C. / Niault, T. / Terenin, I. / Barendse, P. / Koopal, B. / Roosjen, M. / Boeren, S. / Hauryliuk, V. / Jinek, M. / Westphal, A.H. / Swarts, D.C.
History
DepositionFeb 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Similar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein
B: Similar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,25312
Polymers64,1282
Non-polymers1,12410
Water90150
1
A: Similar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6266
Polymers32,0641
Non-polymers5625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Similar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6266
Polymers32,0641
Non-polymers5625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.858, 77.872, 110.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Similar to tr|Q3MCC8|Q3MCC8_ANAVT Hypothetical protein


Mass: 32064.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expression constructed contained His-MBP-TEV site, hence altered amino acids on positions 1-2.
Source: (gene. exp.) Microcystis aeruginosa (bacteria) / Gene: IPF_560 / Production host: Escherichia coli (E. coli) / References: UniProt: A8YDH4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution: -10 mM HEPES-KOH pH 7.5 -250 mM KCl -1 mM DTT Reservoir solution: -0.1 M Bis-Tris pH 5.5 -0.2 M MgCl2 -23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.52→55.23 Å / Num. obs: 23331 / % possible obs: 99.29 % / Redundancy: 2 % / Biso Wilson estimate: 53.39 Å2 / CC1/2: 1 / Rrim(I) all: 0.036 / Net I/σ(I): 17.52
Reflection shellResolution: 2.52→2.61 Å / Mean I/σ(I) obs: 2.42 / Num. unique obs: 2276 / CC1/2: 0.938 / Rrim(I) all: 0.405

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→55.23 Å / SU ML: 0.4644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.89
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2952 1153 4.97 %
Rwork0.2611 22035 -
obs0.2628 23188 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.3 Å2
Refinement stepCycle: LAST / Resolution: 2.52→55.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 42 50 4482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334541
X-RAY DIFFRACTIONf_angle_d0.58626150
X-RAY DIFFRACTIONf_chiral_restr0.0415637
X-RAY DIFFRACTIONf_plane_restr0.0047802
X-RAY DIFFRACTIONf_dihedral_angle_d15.06171712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.630.52321890.41222625X-RAY DIFFRACTION99.29
2.63-2.770.39371340.37932759X-RAY DIFFRACTION99.72
2.77-2.950.4231270.36622715X-RAY DIFFRACTION99.47
2.95-3.170.3771290.32212733X-RAY DIFFRACTION98.62
3.17-3.490.33571460.29932715X-RAY DIFFRACTION98.83
3.49-40.26281440.26142734X-RAY DIFFRACTION99.14
4-5.030.23881450.21592824X-RAY DIFFRACTION99.73
5.04-55.230.23861390.19842930X-RAY DIFFRACTION99.51

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