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- PDB-7chq: AcrIE2 -

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Basic information

Entry
Database: PDB / ID: 7chq
TitleAcrIE2
Componentsanti-CRISPR AcrIE2
KeywordsIMMUNE SYSTEM / AcrIE2 / CRISPR Cascade inhibitor.
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas phage JBD16C (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.33 Å
AuthorsLee, S.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: A 1.3 angstrom high-resolution crystal structure of an anti-CRISPR protein, AcrI E2.
Authors: Lee, S.Y. / Kim, G.E. / Kim, Y.G. / Park, H.H.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-CRISPR AcrIE2


Theoretical massNumber of molelcules
Total (without water)10,4321
Polymers10,4321
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Multi angle light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.960, 47.440, 56.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein anti-CRISPR AcrIE2


Mass: 10432.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD16C (virus) / Gene: JBD16C_30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125RN64
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 28.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8000, 0.2M lithium sulfate, 0.1M sodium acetate pH 4.8

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→28.05 Å / Num. obs: 275146 / % possible obs: 95.49 % / Redundancy: 12.7 % / Rrim(I) all: 0.047 / Net I/σ(I): 31.1
Reflection shellResolution: 1.24→1.27 Å / Num. unique obs: 216131 / Rrim(I) all: 0.369

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Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.33→28.05 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 854 5 %
Rwork0.2071 --
obs0.2081 17089 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms671 0 0 64 735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005685
X-RAY DIFFRACTIONf_angle_d0.745928
X-RAY DIFFRACTIONf_dihedral_angle_d5.49793
X-RAY DIFFRACTIONf_chiral_restr0.084100
X-RAY DIFFRACTIONf_plane_restr0.004125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.410.26141370.26082628X-RAY DIFFRACTION99
1.41-1.520.2491400.23192643X-RAY DIFFRACTION99
1.52-1.680.23021400.19912677X-RAY DIFFRACTION100
1.68-1.920.26171420.20612691X-RAY DIFFRACTION100
1.92-2.420.2291440.19762726X-RAY DIFFRACTION100
2.42-28.050.20741510.20552870X-RAY DIFFRACTION100

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