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- PDB-6jdx: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Ca... -

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Basic information

Entry
Database: PDB / ID: 6jdx
TitleCrystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 preprocessed with protease alpha-Chymotrypsin
Components
  • AcrIIC2
  • CRISPR-associated endonuclease Cas9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CRISPR-Cas9 / Nme1Cas9 / NmeCas9 / anti-CRISPR / AcrIIC2 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
: / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis 8013 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsCheng, Z. / Huang, X. / Sun, W. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725008 China
CitationJournal: Nat Commun / Year: 2019
Title: Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2.
Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / ...Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / Moraes, T.F. / Wang, Y. / Maxwell, K.L.
History
DepositionFeb 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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 1.2Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: AcrIIC2
B: AcrIIC2
C: CRISPR-associated endonuclease Cas9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2474
Polymers37,1853
Non-polymers621
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-18 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.374, 77.236, 107.601
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 AcrIIC2


Mass: 14196.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2QCQ3
#2: Protein CRISPR-associated endonuclease Cas9


Mass: 8791.206 Da / Num. of mol.: 1 / Fragment: truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.9 / Details: 0.1M HEPES pH 7.9, 14% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 21775 / % possible obs: 99.1 % / Redundancy: 10.8 % / CC1/2: 0.915 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.027 / Rrim(I) all: 0.091 / Χ2: 0.969 / Net I/σ(I): 26.6
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1073 / CC1/2: 0.996 / Rpim(I) all: 0.335 / Rrim(I) all: 1.124 / Χ2: 0.937 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JD7

6jd7


Resolution: 2.28→45.003 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2224 820 4.79 %
Rwork0.2079 --
obs0.2087 17113 78.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→45.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 4 61 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192272
X-RAY DIFFRACTIONf_angle_d1.3433061
X-RAY DIFFRACTIONf_dihedral_angle_d23.362869
X-RAY DIFFRACTIONf_chiral_restr0.308322
X-RAY DIFFRACTIONf_plane_restr0.009411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.42290.2388730.2461721X-RAY DIFFRACTION51
2.4229-2.60990.26881010.23461972X-RAY DIFFRACTION58
2.6099-2.87260.27831190.24652516X-RAY DIFFRACTION74
2.8726-3.28810.26951500.23593081X-RAY DIFFRACTION90
3.2881-4.14220.22271870.19143440X-RAY DIFFRACTION100
4.1422-45.01170.18211900.18743563X-RAY DIFFRACTION99

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