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- PDB-9zdx: Dimer of ATPase BrxC containing a Walker B mutation and bound to ... -

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Basic information

Entry
Database: PDB / ID: 9zdx
TitleDimer of ATPase BrxC containing a Walker B mutation and bound to ATP from the Acinetobacter BREX system
ComponentsBREX system P-loop protein BrxC
KeywordsANTIMICROBIAL PROTEIN / Restriction / Bacteriophage / Defense / AlphaFold
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesAcinetobacter (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsDoyle, L.A. / Stoddard, B.L. / Kaiser, B. / Kaiser, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM148166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15 GM140375 United States
Other privateNew England Biolabs United States
CitationJournal: To Be Published
Title: Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system
Authors: Doyle, L.A.
History
DepositionNov 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
C: BREX system P-loop protein BrxC
A: BREX system P-loop protein BrxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,9156
Polymers279,8522
Non-polymers1,0634
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein BREX system P-loop protein BrxC


Mass: 139925.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Gene: SAMN05444586_103019 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BrxC Walker B / Type: COMPLEX
Details: BrxC protein from the Acinetobacter BREX system with a Walker B mutation of Glu to Gln in the ATP binding pocket and bound to ATP
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Acinetobacter (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium chlorideNaCl1
225 mMTris1
31 mMATP1
42 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4131

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionBlob Picker
2cryoSPARC4.5.3particle selectionTemplate Picker
5cryoSPARC4.5.3CTF correctionPatch CTF
8ISOLDEmodel fitting
9Coot0.9.8.93model fitting
10Coot1.1.18model fitting
12cryoSPARC4.5.3initial Euler assignmentAb initio
13cryoSPARC4.5.3initial Euler assignmentHetero Refinement
14cryoSPARC4.5.3final Euler assignmentNon-Uniform Refinement
16cryoSPARC4.5.33D reconstruction
17PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3132271
Details: Blob picking on a 200 micrograph resulted in 112,543 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 477102 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049027
ELECTRON MICROSCOPYf_angle_d0.51812193
ELECTRON MICROSCOPYf_dihedral_angle_d9.211260
ELECTRON MICROSCOPYf_chiral_restr0.0391324
ELECTRON MICROSCOPYf_plane_restr0.0031589

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