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- PDB-8rsv: Rap from bacteriophage Phi3T in presence of pheromone RRGHTAS -

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Basic information

Entry
Database: PDB / ID: 8rsv
TitleRap from bacteriophage Phi3T in presence of pheromone RRGHTAS
Components
  • Pheromone RRGHTAS
  • Rap3T
KeywordsSIGNALING PROTEIN / Rap / Aspartate phosphatase / Phi3T / Bacteriophage
Function / homologyresponse regulator aspartate phosphatase H, N terminal / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / cytoplasm / : / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsFelipe-Ruiz, A. / Zamora-Caballero, S. / Marina, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-137201NB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesFPU19/00433 Spain
CitationJournal: Plos Biol. / Year: 2024
Title: Extracellular proteolysis of tandemly duplicated pheromone propeptides affords additional complexity to bacterial quorum sensing
Authors: Felipe-Ruiz, A. / Zamora-Caballero, S. / Bendori, S.O. / Penades, J.R. / Eldar, A. / Marina, A.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rap3T
B: Rap3T
C: Pheromone RRGHTAS
E: Pheromone RRGHTAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4006
Polymers91,6304
Non-polymers1,7702
Water1,63991
1
A: Rap3T
C: Pheromone RRGHTAS
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 46.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)46,7003
Polymers45,8152
Non-polymers8851
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-0 kcal/mol
Surface area16610 Å2
MethodPISA
2
B: Rap3T
E: Pheromone RRGHTAS
hetero molecules


  • defined by author&software
  • 46.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)46,7003
Polymers45,8152
Non-polymers8851
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-0 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.490, 92.332, 100.670
Angle α, β, γ (deg.)90.000, 106.230, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Rap3T


Mass: 45028.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi3T (virus) / Gene: phi3T_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1P8CWN8
#2: Protein/peptide Pheromone RRGHTAS


Mass: 786.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus phage phi3T (virus)
#3: Chemical ChemComp-A1H22 / Glycerol ethoxylate / 2-[2-[2-[2-[2-[2-[2,3-bis[2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol


Mass: 885.040 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C39H80O21
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% glycerol ethoxylate, 0.2M NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→58.08 Å / Num. obs: 53486 / % possible obs: 97.64 % / Redundancy: 17.8 % / Biso Wilson estimate: 37.37 Å2 / CC1/2: 0.838 / Net I/σ(I): 24.44
Reflection shellResolution: 2.19→2.23 Å / Num. unique obs: 5389 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→58.08 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 2543 4.76 %
Rwork0.2099 50875 -
obs0.2112 53418 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.52 Å2
Refinement stepCycle: LAST / Resolution: 2.19→58.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 27 91 6170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946275
X-RAY DIFFRACTIONf_angle_d0.97518447
X-RAY DIFFRACTIONf_chiral_restr0.0512892
X-RAY DIFFRACTIONf_plane_restr0.00771077
X-RAY DIFFRACTIONf_dihedral_angle_d18.45822339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.230.39961420.32932785X-RAY DIFFRACTION96.47
2.23-2.280.28931400.29862773X-RAY DIFFRACTION97.33
2.28-2.330.32911400.27682854X-RAY DIFFRACTION97.65
2.33-2.380.29331560.26232763X-RAY DIFFRACTION97.49
2.38-2.440.25431390.25622819X-RAY DIFFRACTION97.37
2.44-2.510.32381250.24182814X-RAY DIFFRACTION96.46
2.51-2.580.26981410.24732789X-RAY DIFFRACTION97.05
2.58-2.660.25571460.24472785X-RAY DIFFRACTION96.99
2.66-2.760.31430.24212848X-RAY DIFFRACTION97.65
2.76-2.870.3271400.24292816X-RAY DIFFRACTION97.69
2.87-30.26051500.23352807X-RAY DIFFRACTION97.72
3-3.160.24491260.22722859X-RAY DIFFRACTION97.9
3.16-3.360.2621730.21562835X-RAY DIFFRACTION98.36
3.36-3.620.23821490.19812802X-RAY DIFFRACTION97.84
3.62-3.980.19461230.17922910X-RAY DIFFRACTION98.73
3.98-4.550.20021260.16792872X-RAY DIFFRACTION98.42
4.56-5.740.19891450.1862862X-RAY DIFFRACTION97.79
5.74-58.080.17431390.1812882X-RAY DIFFRACTION96.46
Refinement TLS params.Method: refined / Origin x: 31.4253989875 Å / Origin y: -17.0795627982 Å / Origin z: 25.6847356258 Å
111213212223313233
T0.237604581657 Å2-0.0868101390159 Å20.00377225286786 Å2-0.253138942008 Å20.000225530187541 Å2--0.211707046236 Å2
L0.663126750264 °2-0.634479387818 °20.00814690156335 °2-1.07284012859 °20.0223762705554 °2--0.386203152278 °2
S0.0306626243121 Å °-0.127197512824 Å °-0.00698483161047 Å °-0.0746929695323 Å °0.0631162524326 Å °-0.000442964496033 Å °-0.0188096218764 Å °0.00947002581014 Å °-0.0907418685658 Å °
Refinement TLS groupSelection details: all

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