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- PDB-7c0g: Aca1 in complex with 14bp palindromic DNA target -

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Basic information

Entry
Database: PDB / ID: 7c0g
TitleAca1 in complex with 14bp palindromic DNA target
Components
  • Aca1
  • palindromic DNA target
KeywordsTRANSCRIPTION / CRISPR / anti-CRISPR / anti-CRISPR-associated / DNA binding / autoregulation / Aca1 / complex
Function / homologyLambda repressor-like, DNA-binding domain superfamily / DNA binding / DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, Y.H. / Zhang, L.S. / Wu, B.X. / Huang, H.D.
CitationJournal: To Be Published
Title: Aca1 in complex with 14bp palindromic DNA target
Authors: Liu, Y.H. / Zhang, L.S. / Wu, B.X. / Huang, H.D.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Aca1
B: Aca1
C: palindromic DNA target
D: palindromic DNA target


Theoretical massNumber of molelcules
Total (without water)26,3804
Polymers26,3804
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-27 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.727, 68.727, 206.006
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Aca1


Mass: 8908.148 Da / Num. of mol.: 2
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: DNA chain palindromic DNA target


Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium acetate pH5.0; 20%(w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 12045 / % possible obs: 99.5 % / Redundancy: 27.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 24.333
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.814 / Num. unique obs: 1108 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
PHENIXphenix-1.16-3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C0B

7c0b
PDB Unreleased entry


Resolution: 2.4→35 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2689 --
Rwork0.2174 --
obs0.2201 10774 90.02 %
Displacement parametersBiso mean: 31.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 0 86 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151800
X-RAY DIFFRACTIONf_angle_d1.41252554
X-RAY DIFFRACTIONf_chiral_restr0.0625275
X-RAY DIFFRACTIONf_plane_restr0.0087239
X-RAY DIFFRACTIONf_dihedral_angle_d21.32371002

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