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- PDB-5zw6: Structure of spAimR -

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Basic information

Entry
Database: PDB / ID: 5zw6
TitleStructure of spAimR
Components
  • AimR transcriptional regulator
  • GLY-MET-PRO-ARG-GLY-ALA
KeywordsTRANSCRIPTION REGULATOR / dimer / phage SPbeta
Function / homology: / AimR transcriptional regulator-like / latency-replication decision / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsCheng, W. / Dou, C.
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural and functional insights into the regulation of the lysis-lysogeny decision in viral communities.
Authors: Dou, C. / Xiong, J. / Gu, Y. / Yin, K. / Wang, J. / Hu, Y. / Zhou, D. / Fu, X. / Qi, S. / Zhu, X. / Yao, S. / Xu, H. / Nie, C. / Liang, Z. / Yang, S. / Wei, Y. / Cheng, W.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: GLY-MET-PRO-ARG-GLY-ALA
B: AimR transcriptional regulator
D: GLY-MET-PRO-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)93,2374
Polymers93,2374
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.795, 193.576, 33.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 46029.660 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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O64094
#2: Protein/peptide GLY-MET-PRO-ARG-GLY-ALA


Mass: 588.701 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.: 423 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 3350, 0.1 M sodium citrate pH 4.0, 0.2 M Citric Acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.05→49.024 Å / Num. obs: 62871 / % possible obs: 99.97 % / Redundancy: 18.6 % / Net I/σ(I): 1.3
Reflection shellResolution: 2.05→2.12 Å / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementResolution: 2.05→49.024 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2345 3175 5.05 %
Rwork0.1901 --
obs0.1924 62867 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→49.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 0 423 6961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076658
X-RAY DIFFRACTIONf_angle_d0.9298954
X-RAY DIFFRACTIONf_dihedral_angle_d14.7364080
X-RAY DIFFRACTIONf_chiral_restr0.052978
X-RAY DIFFRACTIONf_plane_restr0.0061148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08060.28211390.23492599X-RAY DIFFRACTION100
2.0806-2.11310.35671320.24392498X-RAY DIFFRACTION100
2.1131-2.14780.28171350.24442518X-RAY DIFFRACTION100
2.1478-2.18480.28061330.22812569X-RAY DIFFRACTION100
2.1848-2.22450.29131200.22232632X-RAY DIFFRACTION100
2.2245-2.26730.2621190.22352511X-RAY DIFFRACTION100
2.2673-2.31360.2811500.22192529X-RAY DIFFRACTION100
2.3136-2.36390.29711390.22792599X-RAY DIFFRACTION100
2.3639-2.41890.30291170.23122556X-RAY DIFFRACTION100
2.4189-2.47940.28251390.22332550X-RAY DIFFRACTION100
2.4794-2.54640.28331220.21842623X-RAY DIFFRACTION100
2.5464-2.62130.28151320.22042554X-RAY DIFFRACTION100
2.6213-2.70590.24521280.22212567X-RAY DIFFRACTION100
2.7059-2.80260.28921610.20842580X-RAY DIFFRACTION100
2.8026-2.91480.26241610.20722538X-RAY DIFFRACTION100
2.9148-3.04750.2631390.20582631X-RAY DIFFRACTION100
3.0475-3.20810.25971240.19782564X-RAY DIFFRACTION100
3.2081-3.40910.25441660.19532611X-RAY DIFFRACTION100
3.4091-3.67220.2131410.18142625X-RAY DIFFRACTION100
3.6722-4.04160.17241490.15072601X-RAY DIFFRACTION100
4.0416-4.6260.17171450.1372651X-RAY DIFFRACTION100
4.626-5.82680.18961480.15912697X-RAY DIFFRACTION100
5.8268-49.03770.17811360.16682889X-RAY DIFFRACTION100

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