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- PDB-6im4: Structural basis of AimP signaling molecule recognition by AimR i... -

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Basic information

Entry
Database: PDB / ID: 6im4
TitleStructural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages
Components
  • AimR transcriptional regulator
  • GLY-MET-PRO-ARG-GLY-ALA
KeywordsPEPTIDE BINDING PROTEIN / Receptor / VIRUS
Function / homology: / latency-replication decision / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOuyang, S.Y.
CitationJournal: Protein Cell / Year: 2019
Title: Structural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages.
Authors: Zhen, X. / Zhou, H. / Ding, W. / Zhou, B. / Xu, X. / Perculija, V. / Chen, C.J. / Chang, M.X. / Choudhary, M.I. / Ouyang, S.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
B: AimR transcriptional regulator
C: GLY-MET-PRO-ARG-GLY-ALA
D: GLY-MET-PRO-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)92,8764
Polymers92,8764
Non-polymers00
Water5,657314
1
A: AimR transcriptional regulator
D: GLY-MET-PRO-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)46,4382
Polymers46,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area18280 Å2
MethodPISA
2
B: AimR transcriptional regulator
C: GLY-MET-PRO-ARG-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)46,4382
Polymers46,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.635, 214.153, 33.852
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: 45849.477 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.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000 magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.928→61.565 Å / Num. obs: 135748 / % possible obs: 96.73 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rsym value: 0.111 / Net I/σ(I): 2
Reflection shellResolution: 1.93→2.03 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→61.565 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 32.32
RfactorNum. reflection% reflection
Rfree0.2683 3763 3.02 %
Rwork0.2192 --
obs0.2207 124677 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→61.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 0 314 6824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086626
X-RAY DIFFRACTIONf_angle_d0.8698910
X-RAY DIFFRACTIONf_dihedral_angle_d6.3024066
X-RAY DIFFRACTIONf_chiral_restr0.049976
X-RAY DIFFRACTIONf_plane_restr0.0051140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.928-1.95240.40521450.34894613X-RAY DIFFRACTION99
1.9524-1.97810.41011400.33364682X-RAY DIFFRACTION100
1.9781-2.00520.35941430.32364617X-RAY DIFFRACTION100
2.0052-2.03390.44021400.3124546X-RAY DIFFRACTION100
2.0339-2.06420.35451280.30784268X-RAY DIFFRACTION92
2.0642-2.09650.3393480.29111576X-RAY DIFFRACTION34
2.0965-2.13080.29971390.26824632X-RAY DIFFRACTION100
2.1308-2.16760.29331410.27034560X-RAY DIFFRACTION100
2.1676-2.2070.29211430.26874590X-RAY DIFFRACTION100
2.207-2.24950.32231510.27114703X-RAY DIFFRACTION99
2.2495-2.29540.31461440.25974533X-RAY DIFFRACTION99
2.2954-2.34530.36471420.26354571X-RAY DIFFRACTION100
2.3453-2.39980.37431450.26344655X-RAY DIFFRACTION99
2.3998-2.45990.34941400.25514525X-RAY DIFFRACTION99
2.4599-2.52640.31671450.25184578X-RAY DIFFRACTION99
2.5264-2.60070.30771440.25294690X-RAY DIFFRACTION99
2.6007-2.68470.31991380.26524500X-RAY DIFFRACTION99
2.6847-2.78060.37811480.25244582X-RAY DIFFRACTION98
2.7806-2.89190.29121410.24794582X-RAY DIFFRACTION100
2.8919-3.02360.31211450.24414662X-RAY DIFFRACTION100
3.0236-3.1830.30221440.23374588X-RAY DIFFRACTION100
3.183-3.38240.27621510.22724717X-RAY DIFFRACTION100
3.3824-3.64350.25961430.20714564X-RAY DIFFRACTION100
3.6435-4.01010.26541460.17914594X-RAY DIFFRACTION100
4.0101-4.59020.18161430.16144613X-RAY DIFFRACTION100
4.5902-5.78250.20131370.17344603X-RAY DIFFRACTION98
5.7825-61.59660.15681490.1554570X-RAY DIFFRACTION99

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