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- PDB-8rst: Rap from bacteriophage Phi3T in presence of pheromone SRGHTS -

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Basic information

Entry
Database: PDB / ID: 8rst
TitleRap from bacteriophage Phi3T in presence of pheromone SRGHTS
Components
  • Rap3T
  • SRGHTS
KeywordsSIGNALING PROTEIN / Rap / Aspartate phosphatase / Phi3T / Bacteriophage
Function / homology
Function and homology information


response regulator aspartate phosphatase H, N terminal / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / tetrahydrofuran / Uncharacterized protein
Similarity search - Component
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 UniversitiesFPU2019/00433 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: SRGHTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7035
Polymers45,6742
Non-polymers1,0293
Water1448
1
A: Rap3T
B: SRGHTS
hetero molecules

A: Rap3T
B: SRGHTS
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 93.4 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)93,40610
Polymers91,3484
Non-polymers2,0596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)60.843, 195.549, 92.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Rap3T


Mass: 45028.223 Da / Num. of mol.: 1
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 SRGHTS


Mass: 645.667 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C39H80O21
#4: Chemical ChemComp-FU1 / tetrahydrofuran


Mass: 72.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH8.5, 15% glycerol ethoxylate, 4% tetrahydrofuran

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.56→48.89 Å / Num. obs: 18149 / % possible obs: 99.92 % / Redundancy: 8 % / Biso Wilson estimate: 82.27 Å2 / CC1/2: 1 / Net I/σ(I): 20.73
Reflection shellResolution: 2.56→2.655 Å / Num. unique obs: 1784 / CC1/2: 0.649

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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: 2.56→48.89 Å / SU ML: 0.3996 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.1494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 946 5.21 %
Rwork0.2089 17197 -
obs0.2112 18143 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.03 Å2
Refinement stepCycle: LAST / Resolution: 2.56→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 22 9 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183106
X-RAY DIFFRACTIONf_angle_d0.38184186
X-RAY DIFFRACTIONf_chiral_restr0.0318448
X-RAY DIFFRACTIONf_plane_restr0.0035531
X-RAY DIFFRACTIONf_dihedral_angle_d13.93161138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.70.33811450.29072396X-RAY DIFFRACTION100
2.7-2.870.32591430.25962404X-RAY DIFFRACTION100
2.87-3.090.33021250.28622439X-RAY DIFFRACTION100
3.09-3.40.30041230.23562454X-RAY DIFFRACTION99.88
3.4-3.890.281280.22062438X-RAY DIFFRACTION99.96
3.89-4.90.22991330.18492496X-RAY DIFFRACTION99.96
4.9-48.890.23021490.19222570X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 18.0073944066 Å / Origin y: 222.101373534 Å / Origin z: 5.85196192956 Å
111213212223313233
T0.628107433632 Å2-0.0194868620659 Å20.0426907986867 Å2-0.68848733179 Å2-0.00948759996623 Å2--0.599754058512 Å2
L1.56870769025 °2-0.243978050423 °20.785923281914 °2-4.25915449162 °2-0.976349528066 °2--3.09665085798 °2
S0.169721281911 Å °0.0432565991621 Å °0.103215728185 Å °-0.00287630701263 Å °-0.0754676195017 Å °0.363282287914 Å °0.757801704103 Å °-0.253422644534 Å °-0.0733244688259 Å °
Refinement TLS groupSelection details: all

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