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- PDB-7b5j: Anti-CRISPR associated (Aca) protein, Aca2 -

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Basic information

Entry
Database: PDB / ID: 7b5j
TitleAnti-CRISPR associated (Aca) protein, Aca2
ComponentsAnti-CRISPR associated (Aca) protein, Aca2
KeywordsDNA BINDING PROTEIN / RNA-binding / DNA-binding / Anti-CRISPR / Regulator / RNA BINDING PROTEIN / Anti-CRISPR associated (Aca) protein
Function / homology
Function and homology information


DNA binding / RNA binding / metal ion binding
Similarity search - Function
Putative cytoplasmic protein / Protein of unknown function DUF1870 / Aca2/YdiL-like / YdiL domain superfamily / Putative cytoplasmic protein / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPectobacterium phage ZF40 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.34 Å
AuthorsUsher, B. / Birkholz, N. / Fineran, P.C. / Blower, T.R.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystal structure of the anti-CRISPR repressor Aca2.
Authors: Usher, B. / Birkholz, N. / Beck, I.N. / Fagerlund, R.D. / Jackson, S.A. / Fineran, P.C. / Blower, T.R.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Aug 25, 2021Group: Database references / Structure summary / Category: database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-CRISPR associated (Aca) protein, Aca2
B: Anti-CRISPR associated (Aca) protein, Aca2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5123
Polymers26,4202
Non-polymers921
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.791, 67.103, 42.240
Angle α, β, γ (deg.)90.000, 106.331, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Anti-CRISPR associated (Aca) protein, Aca2


Mass: 13209.853 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium phage ZF40 (virus) / Gene: ZF40_0030, aca2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9C180
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.07 % / Description: Needle
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M MES, 30% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.34→38.19 Å / Num. obs: 47804 / % possible obs: 99.98 % / Redundancy: 13.5 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1588 / Rpim(I) all: 0.04446 / Rrim(I) all: 0.165 / Net I/σ(I): 10.28
Reflection shellResolution: 1.34→1.388 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4740 / CC1/2: 0.663 / CC star: 0.893 / Rpim(I) all: 0.475 / Rrim(I) all: 1.755 / % possible all: 99.96

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Processing

Software
NameVersionClassification
GDAdata collection
xia2data reduction
Arcimboldophasing
BUCCANEERmodel building
Cootmodel building
PHENIX1.18.2-3874refinement
xia2data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.34→38.19 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 2340 4.9 %
Rwork0.1476 45460 -
obs0.149 47804 99.98 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.31 Å2
Refinement stepCycle: LAST / Resolution: 1.34→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 6 265 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091893
X-RAY DIFFRACTIONf_angle_d1.07022557
X-RAY DIFFRACTIONf_chiral_restr0.069276
X-RAY DIFFRACTIONf_plane_restr0.0075332
X-RAY DIFFRACTIONf_dihedral_angle_d17.4552712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.25011170.21322710X-RAY DIFFRACTION99.72
1.37-1.40.24471440.2072616X-RAY DIFFRACTION100
1.4-1.430.22661480.19412652X-RAY DIFFRACTION100
1.43-1.470.23671370.18572665X-RAY DIFFRACTION99.96
1.47-1.50.23961230.17242674X-RAY DIFFRACTION100
1.5-1.550.22551250.16442661X-RAY DIFFRACTION100
1.55-1.60.23381400.16452685X-RAY DIFFRACTION100
1.6-1.660.17891570.1592652X-RAY DIFFRACTION100
1.66-1.720.20551340.14622662X-RAY DIFFRACTION100
1.72-1.80.20461550.13942658X-RAY DIFFRACTION100
1.8-1.90.1821440.13652679X-RAY DIFFRACTION100
1.9-2.010.1731310.13252680X-RAY DIFFRACTION100
2.01-2.170.15521430.12342659X-RAY DIFFRACTION100
2.17-2.390.13021290.12162691X-RAY DIFFRACTION100
2.39-2.730.17421500.13372679X-RAY DIFFRACTION100
2.73-3.440.15311170.14272707X-RAY DIFFRACTION100
3.44-38.190.16841460.16042730X-RAY DIFFRACTION99.76

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