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- PDB-7ci2: Crystal structure of AcrVA2 in complex with partial MbCpf1 -

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Basic information

Entry
Database: PDB / ID: 7ci2
TitleCrystal structure of AcrVA2 in complex with partial MbCpf1
Components
  • AcrVA2
  • MbCpf1
KeywordsHYDROLASE / anti-CRISPR / CRISPR-Cas / AcrVA2 / Cpf1 / Cas12a / MbCpf1 / MbCas12a / Acr
Function / homologyCRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain / Type V CRISPR-associated protein Cpf1
Function and homology information
Biological speciesMoraxella bovoculi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, P. / Cheng, Z. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91440201 China
National Natural Science Foundation of China (NSFC)31700662 China
CitationJournal: Prog.Biochem.Biophys. / Year: 2021
Title: Structural Study on Anti-CRISPR Protein AcrVA2
Authors: Chen, P. / Sun, W. / Cheng, Z. / Yang, J. / Wang, M. / Wang, J. / Chen, H. / Liu, L. / Wang, Y.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 28, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: AcrVA2
B: AcrVA2
C: MbCpf1
D: MbCpf1


Theoretical massNumber of molelcules
Total (without water)81,3154
Polymers81,3154
Non-polymers00
Water1,20767
1
A: AcrVA2
C: MbCpf1


Theoretical massNumber of molelcules
Total (without water)40,6572
Polymers40,6572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AcrVA2
D: MbCpf1


Theoretical massNumber of molelcules
Total (without water)40,6572
Polymers40,6572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.816, 90.816, 137.679
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 79 or resid 81...
d_2ens_1(chain "B" and (resid 0 through 79 or resid 81 through 93 or resid 95 through 316))
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERTRPA1 - 80
d_12ens_1ASNILEA84 - 96
d_13ens_1ASPASNA100 - 317
d_21ens_1SERTRPB1 - 80
d_22ens_1ASNILEB84 - 96
d_23ens_1ASPASNB100 - 317
d_11ens_2ALAVALC1 - 19
d_21ens_2ALAVALD1 - 19

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999996700362, -0.00168064211047, -0.00194286044258), (-0.00168146237036, -0.999998497874, -0.000420635570197), (-0.0019421505863, 0.000423901028977, -0.999998024178)0.0797059815318, 52.4384540398, -2.95286861648
2given(0.999854791936, 0.0165335524517, 0.00412755212809), (0.0164547674151, -0.99969450576, 0.0184427704826), (0.00443121569782, -0.0183721745334, -0.999821397816)-0.696467159898, 51.8039335421, -2.22973846787

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Components

#1: Protein AcrVA2


Mass: 36879.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovoculi (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide MbCpf1


Mass: 3777.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovoculi (bacteria) / Gene: AAX07_00205 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2B2X7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.035 M Sodium Cacodylate pH 6.5, 12.6 mM MgCl2, 1.58 mM Spermine, 6.3% isopropanol, 15 mM HEPES pH 6.8, 0.75% PEG5K MME,0.2 M NDSB-211

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 31347 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 42.82 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Rrim(I) all: 0.076 / Χ2: 0.887 / Net I/σ(I): 21.7
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1581 / CC1/2: 0.451 / Rpim(I) all: 0.38 / Rrim(I) all: 0.855 / Χ2: 0.787 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CI1

7ci1


Resolution: 2.8→45.41 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 27.0276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 1434 4.96 %
Rwork0.2453 27485 -
obs0.2464 28919 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.92 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 0 67 5308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01765419
X-RAY DIFFRACTIONf_angle_d1.67297381
X-RAY DIFFRACTIONf_chiral_restr0.1279800
X-RAY DIFFRACTIONf_plane_restr0.0108950
X-RAY DIFFRACTIONf_dihedral_angle_d10.7247724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.610112681946
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.87954293592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.4064490.39621032X-RAY DIFFRACTION34.48
2.9-3.020.35981450.34922729X-RAY DIFFRACTION91.79
3.02-3.150.32481950.31872928X-RAY DIFFRACTION99.52
3.15-3.320.2871280.28292977X-RAY DIFFRACTION99.94
3.32-3.530.31721840.28252938X-RAY DIFFRACTION99.94
3.53-3.80.28991140.25853020X-RAY DIFFRACTION99.87
3.8-4.180.23651500.21892961X-RAY DIFFRACTION100
4.18-4.790.23141680.19732965X-RAY DIFFRACTION99.97
4.79-6.030.21691430.20952997X-RAY DIFFRACTION99.9
6.03-45.410.23041580.2112938X-RAY DIFFRACTION99.45

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