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- PDB-6jg9: Crystal structure of AimR in complex with arbitrium peptide -

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Basic information

Entry
Database: PDB / ID: 6jg9
TitleCrystal structure of AimR in complex with arbitrium peptide
Components
  • AimR transcriptional regulator
  • arbitrium peptide
KeywordsPEPTIDE BINDING PROTEIN/PEPTIDE / AimR / Apo / HTH / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-PEPTIDE complex
Function / homology: / AimR transcriptional regulator-like / latency-replication decision / AimR transcriptional regulator
Function and homology information
Biological speciesBacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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

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Assembly

Deposited unit
A: AimR transcriptional regulator
C: arbitrium peptide
B: AimR transcriptional regulator
D: arbitrium peptide


Theoretical massNumber of molelcules
Total (without water)94,3284
Polymers94,3284
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-31 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.926, 213.996, 33.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-528-

HOH

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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: Protein/peptide arbitrium peptide


Mass: 588.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: sodium cacodylate, PEG 8000, NaBr, DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→46.123 Å / Num. obs: 60685 / % possible obs: 100 % / Redundancy: 25.7 % / Net I/σ(I): 39.1
Reflection shellResolution: 2→2.07 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: 1.998→46.123 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2973 4.91 %
Rwork0.2134 --
obs0.2151 60586 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→46.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 0 406 6881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016589
X-RAY DIFFRACTIONf_angle_d1.0948861
X-RAY DIFFRACTIONf_dihedral_angle_d25.0162505
X-RAY DIFFRACTIONf_chiral_restr0.067976
X-RAY DIFFRACTIONf_plane_restr0.0051133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.998-2.03080.3151520.27672604X-RAY DIFFRACTION99
2.0308-2.06580.35951390.26992708X-RAY DIFFRACTION100
2.0658-2.10330.27621450.25192766X-RAY DIFFRACTION100
2.1033-2.14380.30191280.24622630X-RAY DIFFRACTION100
2.1438-2.18760.33241550.25312681X-RAY DIFFRACTION100
2.1876-2.23510.26411550.23972767X-RAY DIFFRACTION100
2.2351-2.28710.24351240.23812669X-RAY DIFFRACTION100
2.2871-2.34430.26971400.2392692X-RAY DIFFRACTION100
2.3443-2.40770.3241440.24432768X-RAY DIFFRACTION100
2.4077-2.47850.2961390.23982664X-RAY DIFFRACTION100
2.4785-2.55850.29771350.23922765X-RAY DIFFRACTION100
2.5585-2.650.29251290.24282696X-RAY DIFFRACTION100
2.65-2.75610.28521540.22952742X-RAY DIFFRACTION100
2.7561-2.88150.29061370.22232729X-RAY DIFFRACTION100
2.8815-3.03340.25361330.22452777X-RAY DIFFRACTION100
3.0334-3.22340.26931250.21832745X-RAY DIFFRACTION100
3.2234-3.47220.22761550.21092751X-RAY DIFFRACTION100
3.4722-3.82140.23371440.20292796X-RAY DIFFRACTION100
3.8214-4.3740.20621380.1712798X-RAY DIFFRACTION100
4.374-5.50940.20851640.18522845X-RAY DIFFRACTION100
5.5094-46.13540.18631380.19053020X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.5016 Å / Origin y: 42.5346 Å / Origin z: 14.3026 Å
111213212223313233
T0.2091 Å2-0.0047 Å2-0.0268 Å2-0.2011 Å20.0013 Å2--0.2378 Å2
L0.6329 °20.3743 °20.1189 °2-1.5255 °20.436 °2--0.2628 °2
S-0.0319 Å °0.0356 Å °0.2672 Å °-0.0631 Å °-0.0846 Å °0.5008 Å °-0.0601 Å °-0.0171 Å °0.0558 Å °
Refinement TLS groupSelection details: all

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