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- PDB-6jg8: Crystal structure of AimR in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6jg8
TitleCrystal structure of AimR in complex with DNA
Components
  • (DNA (31-MER)) x 2
  • AimR transcriptional regulator
KeywordsPEPTIDE BINDING PROTEIN/DNA / AimR / Apo / HTH / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-DNA complex
Function / homology: / AimR transcriptional regulator-like / latency-replication decision / DNA / DNA (> 10) / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsGuan, Z.Y. / Pei, K. / Zou, T.T.
CitationJournal: Cell Discov / Year: 2019
Title: Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage.
Authors: Guan, Z.Y. / Pei, K. / Wang, J. / Cui, Y.Q. / Zhu, X. / Su, X. / Zhou, Y.B. / Zhang, D.L. / Tang, C. / Yin, P. / Liu, Z. / Zou, T.T.
History
DepositionFeb 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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: AimR transcriptional regulator
B: AimR transcriptional regulator
C: DNA (31-MER)
D: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)112,2064
Polymers112,2064
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-64 kcal/mol
Surface area43770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.007, 98.007, 159.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein AimR transcriptional regulator / Arbitrium communication peptide receptor / YopK protein


Mass: 46575.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPbeta (virus) / Gene: aimR, yopK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64094
#2: DNA chain DNA (31-MER)


Mass: 9523.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus)
#3: DNA chain DNA (31-MER)


Mass: 9532.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: sodium cacodylate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.097→45 Å / Num. obs: 97895 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 1.7
Reflection shellResolution: 2.097→2.13 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XYB

5xyb


Resolution: 2.097→42.273 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.41
RfactorNum. reflection% reflection
Rfree0.2219 4338 4.94 %
Rwork0.2103 --
obs0.2109 87785 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→42.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 1227 0 257 7905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097923
X-RAY DIFFRACTIONf_angle_d1.06610928
X-RAY DIFFRACTIONf_dihedral_angle_d27.9243085
X-RAY DIFFRACTIONf_chiral_restr0.0541206
X-RAY DIFFRACTIONf_plane_restr0.0051186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0969-2.12080.31911280.30682744X-RAY DIFFRACTION98
2.1208-2.14570.31831190.30772781X-RAY DIFFRACTION100
2.1457-2.17190.33331270.31752811X-RAY DIFFRACTION100
2.1719-2.19940.32261350.30012775X-RAY DIFFRACTION100
2.1994-2.22830.35571400.2982859X-RAY DIFFRACTION100
2.2283-2.25880.30951530.28882740X-RAY DIFFRACTION100
2.2588-2.29110.29911430.28422758X-RAY DIFFRACTION100
2.2911-2.32530.32641480.28912810X-RAY DIFFRACTION100
2.3253-2.36160.30631480.28642741X-RAY DIFFRACTION100
2.3616-2.40030.31671410.292820X-RAY DIFFRACTION100
2.4003-2.44170.32311440.28722792X-RAY DIFFRACTION100
2.4417-2.48610.29771370.28292755X-RAY DIFFRACTION100
2.4861-2.53390.32281650.2882745X-RAY DIFFRACTION99
2.5339-2.58570.30281450.27822797X-RAY DIFFRACTION100
2.5857-2.64190.3281600.2832790X-RAY DIFFRACTION100
2.6419-2.70330.30691660.27732732X-RAY DIFFRACTION100
2.7033-2.77090.32231460.29682808X-RAY DIFFRACTION100
2.7709-2.84580.29521390.27182780X-RAY DIFFRACTION100
2.8458-2.92950.27911740.25592750X-RAY DIFFRACTION100
2.9295-3.02410.27721330.25072807X-RAY DIFFRACTION100
3.0241-3.13210.26431230.25212825X-RAY DIFFRACTION100
3.1321-3.25750.241310.24892774X-RAY DIFFRACTION99
3.2575-3.40570.24961690.22442729X-RAY DIFFRACTION99
3.4057-3.58510.21731630.21522743X-RAY DIFFRACTION99
3.5851-3.80960.1871380.19032780X-RAY DIFFRACTION99
3.8096-4.10350.17431630.17142792X-RAY DIFFRACTION100
4.1035-4.51610.16661480.15282771X-RAY DIFFRACTION100
4.5161-5.16860.16741630.15552786X-RAY DIFFRACTION99
5.1686-6.5080.1871260.18042803X-RAY DIFFRACTION99
6.508-42.28110.11931230.12942849X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.395 Å / Origin y: 38.3412 Å / Origin z: 4.7908 Å
111213212223313233
T0.3742 Å2-0.0118 Å20.0186 Å2-0.5133 Å20.0469 Å2--0.4014 Å2
L0.8045 °2-0.0655 °2-0.0521 °2--0.1139 °20.0472 °2--0.0007 °2
S0.0399 Å °-0.0296 Å °-0.2176 Å °0.02 Å °-0.0609 Å °-0.0564 Å °-0.0478 Å °0.0717 Å °0.02 Å °
Refinement TLS groupSelection details: all

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