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- PDB-7xmw: Crystal structure of anti-CRISPR protein AcrVIA2 -

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Basic information

Entry
Database: PDB / ID: 7xmw
TitleCrystal structure of anti-CRISPR protein AcrVIA2
ComponentsAcrVIA2
KeywordsANTIVIRAL PROTEIN / a bacteria antiviral protein
Function / homologymetal ion binding / SELENIUM ATOM / Uncharacterized protein
Function and homology information
Biological speciesLeptotrichia wadei
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsYan, X. / Li, X. / Song, G.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structure of AcrVIA2 and its binding mechanism to CRISPR-Cas13a.
Authors: Song, G. / Li, X. / Wang, Z. / Dong, C. / Xie, X. / Yan, X.
History
DepositionApr 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcrVIA2
B: AcrVIA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6237
Polymers16,7042
Non-polymers9195
Water00
1
A: AcrVIA2
B: AcrVIA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5446
Polymers16,7042
Non-polymers8404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.377, 123.377, 123.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Space group name HallP423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y

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Components

#1: Protein AcrVIA2


Mass: 8352.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia wadei (strain F0279) (bacteria)
Strain: F0279 / Gene: HMPREF9015_01064 / Production host: Escherichia coli (E. coli) / References: UniProt: U2Q5N5
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Se
Has ligand of interestN
Has protein modificationN

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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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion / Details: TRIS hydrochloride, ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.59→41.13 Å / Num. obs: 9880 / % possible obs: 92.89 % / Redundancy: 2 % / Biso Wilson estimate: 84.03 Å2 / CC1/2: 0.999 / Net I/σ(I): 51.14
Reflection shellResolution: 2.59→2.683 Å / Num. unique obs: 535 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→41.13 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.2511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3067 444 4.51 %
Rwork0.2522 9411 -
obs0.2543 9855 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.43 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 51 0 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131171
X-RAY DIFFRACTIONf_angle_d1.07741563
X-RAY DIFFRACTIONf_chiral_restr0.0497156
X-RAY DIFFRACTIONf_plane_restr0.0054201
X-RAY DIFFRACTIONf_dihedral_angle_d9.1356190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.960.34321270.32892672X-RAY DIFFRACTION81.53
2.96-3.730.31941670.29163301X-RAY DIFFRACTION99.97
3.73-41.130.29641500.23153438X-RAY DIFFRACTION97.1
Refinement TLS params.Method: refined / Origin x: 32.6340708388 Å / Origin y: 35.9876254129 Å / Origin z: 11.8229401988 Å
111213212223313233
T0.840432064398 Å20.185756411963 Å20.10834436684 Å2-0.711559680182 Å2-0.0979562363387 Å2--0.895263055368 Å2
L0.627781849846 °2-0.0514807798229 °20.314612595341 °2--0.802062106412 °2-0.228744190033 °2--0.214908386439 °2
S-0.0256016825218 Å °0.040139473279 Å °-0.0849607167623 Å °-0.0561069212294 Å °-0.0726463994477 Å °0.0804124848896 Å °-0.0478012178062 Å °0.039928560947 Å °0.127094371327 Å °
Refinement TLS groupSelection details: all

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