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- PDB-7vjo: Pectobacterium phage ZF40 apo-Aca2 -

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Basic information

Entry
Database: PDB / ID: 7vjo
TitlePectobacterium phage ZF40 apo-Aca2
Componentsanti-CRISPR-associated protein Aca2
KeywordsTRANSCRIPTION / anti-crispr / Aca2 / anti-crispr-associated protein / crispr / repression
Function / homologyProtein of unknown function DUF1870 / Domain of unknown function (DUF1870) / YdiL domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / metal ion binding / DUF1870 family protein
Function and homology information
Biological speciesPectobacterium phage ZF40 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 20, 2021ID: 7CQ8
Revision 1.0Oct 20, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: anti-CRISPR-associated protein Aca2
A: anti-CRISPR-associated protein Aca2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6738
Polymers27,5052
Non-polymers1686
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-49 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.201, 34.566, 81.299
Angle α, β, γ (deg.)90.000, 124.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

21A-415-

HOH

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Components

#1: Protein anti-CRISPR-associated protein Aca2


Mass: 13752.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium phage ZF40 (virus) / Gene: ZF40_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: H9C180
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 20% PEG 8000

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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: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 63673 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.968 / Net I/σ(I): 18.28
Reflection shellResolution: 1.23→1.25 Å / Num. unique obs: 3175 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CQ9

7cq9
PDB Unreleased entry


Resolution: 1.31→39.601 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 2628 5.07 %
Rwork0.1556 49230 -
obs0.1571 51858 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.84 Å2 / Biso mean: 20.1201 Å2 / Biso min: 9.35 Å2
Refinement stepCycle: final / Resolution: 1.31→39.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 6 467 2352
Biso mean--25.65 30.54 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071927
X-RAY DIFFRACTIONf_angle_d0.9542608
X-RAY DIFFRACTIONf_chiral_restr0.068282
X-RAY DIFFRACTIONf_plane_restr0.007341
X-RAY DIFFRACTIONf_dihedral_angle_d12.966724
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.31-1.33380.22541470.2087240591
1.3338-1.35950.24641400.1968234290
1.3595-1.38720.22961240.1939261398
1.3872-1.41740.23611340.1861258498
1.4174-1.45040.22461280.1838259399
1.4504-1.48660.20331640.174257899
1.4866-1.52680.19661350.1618261198
1.5268-1.57180.2041160.1588254395
1.5718-1.62250.21191410.1605258198
1.6225-1.68050.17081580.1512616100
1.6805-1.74780.15471200.14592683100
1.7478-1.82730.19341280.1466268099
1.8273-1.92370.18331370.1565262999
1.9237-2.04420.18241420.1491256496
2.0442-2.2020.15581320.1332263399
2.202-2.42360.19751620.149261198
2.4236-2.77420.17771240.1503263297
2.7742-3.49490.16791420.1518265298
3.4949-39.60.18581540.1627268097

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