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- PDB-6jd7: Crystal structure of anti-CRISPR protein AcrIIC2 dimer -

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Basic information

Entry
Database: PDB / ID: 6jd7
TitleCrystal structure of anti-CRISPR protein AcrIIC2 dimer
ComponentsAcrIIC2
KeywordsHYDROLASE INHIBITOR / CRISPR-Cas9 / Nme1Cas9 / NmeCas9 / anti-CRISPR / AcrIIC2
Function / homologyACETATE ION / :
Function and homology information
Biological speciesNeisseria meningitidis 8013 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsCheng, Z. / Huang, X. / Sun, W. / Wang, Y.L.
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
DepositionJan 31, 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 1.2Dec 30, 2020Group: Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / struct_conn / struct_keywords
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Mar 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: AcrIIC2
B: AcrIIC2
C: AcrIIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6745
Polymers42,5903
Non-polymers832
Water2,306128
1
A: AcrIIC2
B: AcrIIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4774
Polymers28,3942
Non-polymers832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-10 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: AcrIIC2

C: AcrIIC2


Theoretical massNumber of molelcules
Total (without water)28,3942
Polymers28,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2630 Å2
ΔGint-14 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.559, 73.532, 81.087
Angle α, β, γ (deg.)90.00, 129.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AcrIIC2


Mass: 14196.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: CIJ84_02100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2QCQ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: counter-diffusion / pH: 6.5
Details: 0.05M Na cacodylate pH 6.5, 0.1M Ammonium acetate, 0.015M Mg acetate, 10% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 17826 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 0.972 / Net I/σ(I): 19.7
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.57 / Num. unique obs: 855 / CC1/2: 0.959 / Rrim(I) all: 0.321 / Χ2: 0.905 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→39.992 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 937 5.41 %
Rwork0.1939 --
obs0.1941 17318 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→39.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 5 128 2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022848
X-RAY DIFFRACTIONf_angle_d1.4793854
X-RAY DIFFRACTIONf_dihedral_angle_d26.2151057
X-RAY DIFFRACTIONf_chiral_restr0.279400
X-RAY DIFFRACTIONf_plane_restr0.008525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.57920.24421310.24172139X-RAY DIFFRACTION91
2.5792-2.74070.25481350.22642322X-RAY DIFFRACTION99
2.7407-2.95230.21411170.21812389X-RAY DIFFRACTION100
2.9523-3.24930.1921370.21092373X-RAY DIFFRACTION100
3.2493-3.71920.17041590.18722344X-RAY DIFFRACTION100
3.7192-4.68460.16691060.15922412X-RAY DIFFRACTION100
4.6846-39.99750.20871520.19252402X-RAY DIFFRACTION99

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