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- PDB-7x31: solution structure of an anti-CRISPR protein -

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Basic information

Entry
Database: PDB / ID: 7x31
Titlesolution structure of an anti-CRISPR protein
ComponentsAnti-CRISPR protein (AcrIIC1)
KeywordsVIRAL PROTEIN / anti-CRISPR
Function / homologyAnti-CRISPR protein (AcrIIC1)
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhao, Y. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900863 China
CitationJournal: Nat Commun / Year: 2022
Title: A redox switch regulates the assembly and anti-CRISPR activity of AcrIIC1.
Authors: Zhao, Y. / Hu, J. / Yang, S.S. / Zhong, J. / Liu, J. / Wang, S. / Jiao, Y. / Jiang, F. / Zhai, R. / Ren, B. / Cong, H. / Zhu, Y. / Han, F. / Zhang, J. / Xu, Y. / Huang, Z. / Zhang, S. / Yang, F.
History
DepositionFeb 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
A: Anti-CRISPR protein (AcrIIC1)


Theoretical massNumber of molelcules
Total (without water)9,6381
Polymers9,6381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anti-CRISPR protein (AcrIIC1)


Mass: 9637.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TCG3

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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
123isotropic12D 1H-13C HSQC
131isotropic13D 1H-15N NOESY-HSQC
142isotropic13D 1H-13C NOESY-HSQC
152isotropic13D CBCA(CO)NH
162isotropic13D HN(CA)CB
172isotropic13D HNCO
182isotropic13D HNCA
192isotropic13D HBHA(CO)NH
1103isotropic13D (H)CCH-TOCSY
1113isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] protein, 20 mM TRIS, 100 mM sodium chloride, 90% H2O/10% D2O15N90% H2O/10% D2O
solution21 mM [U-13C; U-15N] protein, 20 mM TRIS, 100 mM sodium chloride, 90% H2O/10% D2O15N13C90% H2O/10% D2O
solution31 mM [U-13C; U-15N] protein, 20 mM TRIS, 100 mM sodium chloride, 100% D2O15N13C_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-15N]1
20 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
1 mMprotein[U-13C; U-15N]2
20 mMTRISnatural abundance2
100 mMsodium chloridenatural abundance2
1 mMprotein[U-13C; U-15N]3
20 mMTRISnatural abundance3
100 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 100 mM / Label: conditions_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: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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