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- PDB-5y6a: Crystal structure of the anti-CRISPR protein, AcrIIA1 -

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Basic information

Entry
Database: PDB / ID: 5y6a
TitleCrystal structure of the anti-CRISPR protein, AcrIIA1
Componentschain A and B
KeywordsVIRAL PROTEIN / Unknown function
Function / homologyLambda repressor-like, DNA-binding domain superfamily / DNA binding / Gp23
Function and homology information
Biological speciesListeria monocytogenes J0161 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKa, D. / An, S.Y. / Suh, J.Y. / Bae, E.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01111201 Korea, Republic Of
the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and TechnologyNRF-2016R1D1A1A09916821 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Crystal structure of an anti-CRISPR protein, AcrIIA1
Authors: Ka, D. / An, S.Y. / Suh, J.Y. / Bae, E.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
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: chain A and B
B: chain A and B


Theoretical massNumber of molelcules
Total (without water)34,9362
Polymers34,9362
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-17 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.435, 55.420, 46.504
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein chain A and B


Mass: 17468.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes J0161 (bacteria)
Gene: LMOG_03146 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A8ATW7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M Mg Acetate, 13 % (w/v) PEG6000, 0.05 M Na cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21982 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.112 / Rsym value: 0.178 / Net I/σ(I): 19.86
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y69

5y69


Resolution: 2→28.326 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.2284 1100 5 %
Rwork0.1827 --
obs0.1851 21980 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 0 135 2527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072428
X-RAY DIFFRACTIONf_angle_d0.9023264
X-RAY DIFFRACTIONf_dihedral_angle_d14.882936
X-RAY DIFFRACTIONf_chiral_restr0.035378
X-RAY DIFFRACTIONf_plane_restr0.003414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.991-2.08160.30431250.23012379X-RAY DIFFRACTION91
2.0816-2.19130.22961380.2032633X-RAY DIFFRACTION100
2.1913-2.32860.27031390.20292629X-RAY DIFFRACTION100
2.3286-2.50830.25871370.1982616X-RAY DIFFRACTION100
2.5083-2.76050.25471390.19592636X-RAY DIFFRACTION100
2.7605-3.15950.25591390.19682636X-RAY DIFFRACTION100
3.1595-3.97880.21931400.17642655X-RAY DIFFRACTION100
3.9788-28.32870.19261430.1612696X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.32310.84830.75923.53410.99348.6510.08970.573-0.1761-0.19460.2513-0.07970.6188-0.5014-0.3150.3377-0.0376-0.03290.32960.01350.210430.34748.209145.895
28.9299-3.9898-1.57925.52841.07013.85580.32410.5428-0.5435-0.3555-0.2116-0.46870.2940.378-0.11050.2610.0155-0.01980.3795-0.03780.441952.013641.648561.0967
36.2081.1851.72992.67160.76275.3803-0.0246-0.13690.1830.19340.00940.1585-0.1304-0.3520.03550.25630.00970.02290.17080.00990.15627.046954.840167.4858
47.53561.6628-0.29055.9508-1.34515.7334-0.0550.2776-0.2449-0.1839-0.14220.41330.1893-0.470.18420.20840.0156-0.01830.3695-0.00870.32464.117243.588356.9587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 149 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 72 )
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 149 )

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