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- PDB-5y24: Crystal structure of AimR from Bacillus phage SPbeta in complex w... -

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Basic information

Entry
Database: PDB / ID: 5y24
TitleCrystal structure of AimR from Bacillus phage SPbeta in complex with its signalling peptide
Components
  • AimR transcriptional regulator
  • GLY-MET-PRO-ARG-GLY-ALA
KeywordsPEPTIDE BINDING PROTEIN / DNA binding protein / complex with peptide
Function / homology: / AimR transcriptional regulator-like / latency-replication decision / BROMIDE ION / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.922 Å
AuthorsWang, Q. / Guan, Z.Y. / Zou, T.T. / Yin, P.
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural basis of the arbitrium peptide-AimR communication system in the phage lysis-lysogeny decision.
Authors: Wang, Q. / Guan, Z. / Pei, K. / Wang, J. / Liu, Z. / Yin, P. / Peng, D. / Zou, T.
History
DepositionJul 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4259
Polymers96,0254
Non-polymers4005
Water8,971498
1
A: AimR transcriptional regulator
C: GLY-MET-PRO-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2525
Polymers48,0132
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-10 kcal/mol
Surface area16870 Å2
MethodPISA
2
B: AimR transcriptional regulator
D: GLY-MET-PRO-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1724
Polymers48,0132
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.550, 119.605, 214.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 47423.805 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) / Strain (production host): BL21(DE3) / 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.) Bacillus phage SPbeta (virus)
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, dithiothreitol, Sodium Bromine, Sodium Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.92014 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92014 Å / Relative weight: 1
ReflectionResolution: 1.92→45 Å / Num. obs: 67332 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 39.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data processing
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.922→39.196 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.69
RfactorNum. reflection% reflection
Rfree0.2489 3298 4.91 %
Rwork0.2163 --
obs0.2179 67233 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.922→39.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5819 0 5 498 6322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095918
X-RAY DIFFRACTIONf_angle_d0.9767952
X-RAY DIFFRACTIONf_dihedral_angle_d25.2412246
X-RAY DIFFRACTIONf_chiral_restr0.064877
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9215-1.9490.32011280.24652653X-RAY DIFFRACTION99
1.949-1.97810.32111550.25622628X-RAY DIFFRACTION100
1.9781-2.0090.28941350.24222571X-RAY DIFFRACTION100
2.009-2.04190.33221580.22922605X-RAY DIFFRACTION100
2.0419-2.07710.26311490.23172621X-RAY DIFFRACTION100
2.0771-2.11490.27231430.23612630X-RAY DIFFRACTION100
2.1149-2.15560.29681200.23082593X-RAY DIFFRACTION100
2.1556-2.19960.27341470.2312643X-RAY DIFFRACTION100
2.1996-2.24740.25061420.21462677X-RAY DIFFRACTION100
2.2474-2.29970.27291210.22132602X-RAY DIFFRACTION100
2.2997-2.35720.28391480.2292628X-RAY DIFFRACTION100
2.3572-2.42090.3081470.22842648X-RAY DIFFRACTION100
2.4209-2.49210.29541200.22042650X-RAY DIFFRACTION100
2.4921-2.57250.26211400.22522687X-RAY DIFFRACTION100
2.5725-2.66450.28491090.22562630X-RAY DIFFRACTION100
2.6645-2.77110.25781070.22572717X-RAY DIFFRACTION100
2.7711-2.89720.2961350.21982649X-RAY DIFFRACTION100
2.8972-3.04990.24381500.22772703X-RAY DIFFRACTION100
3.0499-3.24090.28351400.22352643X-RAY DIFFRACTION100
3.2409-3.4910.2351310.21022705X-RAY DIFFRACTION100
3.491-3.8420.21621370.19772708X-RAY DIFFRACTION100
3.842-4.39730.19691570.17482681X-RAY DIFFRACTION99
4.3973-5.53770.19861430.1922775X-RAY DIFFRACTION99
5.5377-39.20430.25181360.24612888X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -70.204 Å / Origin y: 121.8619 Å / Origin z: 256.141 Å
111213212223313233
T0.2237 Å2-0.0387 Å20.0276 Å2-0.2629 Å2-0.0061 Å2--0.2498 Å2
L-0.0361 °20.0614 °20.2434 °2-0.5353 °20.3482 °2--1.2956 °2
S0.0563 Å °-0.0505 Å °0.006 Å °0.1904 Å °-0.0371 Å °0.0417 Å °0.3818 Å °-0.1074 Å °-0.0256 Å °
Refinement TLS groupSelection details: all

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