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

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Basic information

Entry
Database: PDB / ID: 9iab
TitleStructure of the Argonaute-associated Cas4 family protein 1 (ACE1) from Chroococcidiopsis thermalis (CtACE1)
ComponentsPD-(D/E)XK endonuclease-like domain-containing 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 / PD-(D/E)XK endonuclease-like domain-containing protein
Function and homology information
Biological speciesChroococcidiopsis thermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 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: PD-(D/E)XK endonuclease-like domain-containing protein
B: PD-(D/E)XK endonuclease-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,77813
Polymers62,8132
Non-polymers1,96511
Water7,116395
1
A: PD-(D/E)XK endonuclease-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5338
Polymers31,4071
Non-polymers1,1267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PD-(D/E)XK endonuclease-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2455
Polymers31,4071
Non-polymers8384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.910, 44.950, 74.060
Angle α, β, γ (deg.)100.170, 92.220, 105.870
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein PD-(D/E)XK endonuclease-like domain-containing protein


Mass: 31406.740 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.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_5200 / Production host: Escherichia coli (E. coli) / References: UniProt: K9U6V4
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: -7.5 mg/ml CtACE1 -10 mM HEPES-KOH pH7.5 -250 mM KCl -1 mM DTT Reservoir solution: -0.1 M MES pH 6-7 -0.2 M (NH4)2SO4 -20-25% PEG MME 5K
PH range: 6-7

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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: 1.57→43.02 Å / Num. obs: 144407 / % possible obs: 99.29 % / Redundancy: 7 % / CC1/2: 0.999 / Rrim(I) all: 0.034 / Net I/σ(I): 31.65
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 7.1 % / Num. unique obs: 7241 / CC1/2: 0.918 / Rrim(I) all: 0.559 / % possible all: 94.57

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.57→43.02 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 3917 2.71 %
Rwork0.1859 140490 -
obs0.1863 144407 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 1.57→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 89 395 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824546
X-RAY DIFFRACTIONf_angle_d1.10756158
X-RAY DIFFRACTIONf_chiral_restr0.0579656
X-RAY DIFFRACTIONf_plane_restr0.0149788
X-RAY DIFFRACTIONf_dihedral_angle_d13.48331732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.3511360.27374995X-RAY DIFFRACTION92.75
1.59-1.610.28411420.26755030X-RAY DIFFRACTION93.32
1.61-1.630.25721340.25844859X-RAY DIFFRACTION93.47
1.63-1.650.24011360.25414951X-RAY DIFFRACTION93.48
1.65-1.680.26331400.24825000X-RAY DIFFRACTION94.24
1.68-1.70.32031390.23214966X-RAY DIFFRACTION93.84
1.7-1.730.2651440.23545143X-RAY DIFFRACTION94.44
1.73-1.760.25371360.23184838X-RAY DIFFRACTION94.31
1.76-1.790.23461410.24065038X-RAY DIFFRACTION93.99
1.79-1.820.27651370.2444997X-RAY DIFFRACTION94.48
1.82-1.850.30271400.24145058X-RAY DIFFRACTION94.61
1.85-1.890.28991410.22995006X-RAY DIFFRACTION94.89
1.89-1.930.23091410.21795014X-RAY DIFFRACTION94.73
1.93-1.980.20271400.19864997X-RAY DIFFRACTION94.71
1.98-2.030.2191380.19585059X-RAY DIFFRACTION95.01
2.03-2.080.23351390.18874991X-RAY DIFFRACTION95.14
2.08-2.140.17441440.19445101X-RAY DIFFRACTION95.05
2.14-2.210.22191380.18464970X-RAY DIFFRACTION94.59
2.21-2.290.22391350.18475029X-RAY DIFFRACTION95.28
2.29-2.380.26341430.17425057X-RAY DIFFRACTION94.68
2.38-2.490.18141400.18325030X-RAY DIFFRACTION94.76
2.49-2.620.22311400.17755055X-RAY DIFFRACTION95.46
2.62-2.790.21291410.19465075X-RAY DIFFRACTION95.6
2.79-30.26371420.19225110X-RAY DIFFRACTION95.28
3-3.310.19981390.1874899X-RAY DIFFRACTION94.27
3.31-3.780.17141420.16125049X-RAY DIFFRACTION94.38
3.78-4.760.13171420.14895078X-RAY DIFFRACTION96.52
4.77-43.020.15541470.18335095X-RAY DIFFRACTION95.73

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