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- PDB-5xn4: Anti-CRISPR protein AcrIIA4 -

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Basic information

Entry
Database: PDB / ID: 5xn4
TitleAnti-CRISPR protein AcrIIA4
ComponentsAnti-CRISPR AcrIIA4
KeywordsHYDROLASE INHIBITOR / Cas9 Inhibitor
Function / homologyAnti-CRISPR protein AcrIIA4
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuh, J.-Y. / Kim, I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Cooperative Research Program for Agriculture Science & Technology Development, Rural Development AdministrationPJ011112 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2018
Title: Solution structure and dynamics of anti-CRISPR AcrIIA4, the Cas9 inhibitor.
Authors: Kim, I. / Jeong, M. / Ka, D. / Han, M. / Kim, N.K. / Bae, E. / Suh, J.Y.
History
DepositionMay 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Anti-CRISPR AcrIIA4


Theoretical massNumber of molelcules
Total (without water)10,1821
Polymers10,1821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anti-CRISPR AcrIIA4


Mass: 10182.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A247D711*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HBHA(CO)NH
151isotropic13D HNCO
161isotropic13D 1H-13C NOESY
171isotropic13D 1H-13C NOESY aromatic
181isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 2.0 mM [U-99% 13C; U-99% 15N] AcrIIA4, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 mM / Component: AcrIIA4 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
PIPPGarrettchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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