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- PDB-7vjn: Crystal structure of anti-CRISPR-associated protein Aca1 in Pseud... -

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Basic information

Entry
Database: PDB / ID: 7vjn
TitleCrystal structure of anti-CRISPR-associated protein Aca1 in Pseudomonas phage JBD30
Componentsanti-CRISPR-associated protein Aca1
KeywordsTRANSCRIPTION / DNA binding / autoregulation
Function / homologyLambda repressor-like, DNA-binding domain superfamily / DNA binding / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsLiu, Y.H. / Zhang, L.S. / Wu, B.X. / Huang, H.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.
Authors: Liu, Y. / Zhang, L. / Guo, M. / Chen, L. / Wu, B. / Huang, H.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 13, 2021ID: 7FA2
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
B: anti-CRISPR-associated protein Aca1
A: anti-CRISPR-associated protein Aca1


Theoretical massNumber of molelcules
Total (without water)18,6072
Polymers18,6072
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-12 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.698, 50.435, 64.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein anti-CRISPR-associated protein Aca1


Mass: 9303.537 Da / Num. of mol.: 2 / Mutation: C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD30 (virus) / Gene: JBD30_036 / Production host: Escherichia coli (E. coli) / References: UniProt: L7P845
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M di-potassium hydrogen phosphate, 20% (w/v) PEG 3350

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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: Dec 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.799→40 Å / Num. obs: 14457 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 1407 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000v705cdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FA3

7fa3


Resolution: 1.799→39.829 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 729 5.06 %
Rwork0.1904 13672 -
obs0.1917 14401 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.99 Å2 / Biso mean: 37.2274 Å2 / Biso min: 18.14 Å2
Refinement stepCycle: final / Resolution: 1.799→39.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 131 1235
Biso mean---42.91 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131129
X-RAY DIFFRACTIONf_angle_d1.2111532
X-RAY DIFFRACTIONf_chiral_restr0.07162
X-RAY DIFFRACTIONf_plane_restr0.008206
X-RAY DIFFRACTIONf_dihedral_angle_d2.106704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7992-1.93810.27881240.24267899
1.9381-2.13310.25661520.20012686100
2.1331-2.44170.21951430.1938269899
2.4417-3.07610.21481390.19862765100
3.0761-39.8290.19991710.17832845100

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