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- PDB-8rsu: Rap from bacteriophage Phi3T in presence of pheromone RRGHTA -

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Basic information

Entry
Database: PDB / ID: 8rsu
TitleRap from bacteriophage Phi3T in presence of pheromone RRGHTA
Components
  • Pheromone RRGHTA
  • 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 / : / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rap3T
B: Pheromone RRGHTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6133
Polymers45,7282
Non-polymers8851
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint1 kcal/mol
Surface area16510 Å2
Unit cell
Length a, b, c (Å)61.070, 194.031, 93.534
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 Pheromone RRGHTA


Mass: 699.783 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH8.5, 12.5% glycerol ethoxylate, 6% 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: 2.4→58.25 Å / Num. obs: 22076 / % possible obs: 99.86 % / Redundancy: 8 % / Biso Wilson estimate: 64.2 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.72
Reflection shellResolution: 2.4→2.491 Å / Num. unique obs: 2166 / CC1/2: 0.714

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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: 2.4→58.25 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 1142 5.18 %
Rwork0.2179 20919 -
obs0.2199 22061 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→58.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 11 27 3077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693125
X-RAY DIFFRACTIONf_angle_d0.99714201
X-RAY DIFFRACTIONf_chiral_restr0.0543442
X-RAY DIFFRACTIONf_plane_restr0.007533
X-RAY DIFFRACTIONf_dihedral_angle_d18.02381176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.37221370.362576X-RAY DIFFRACTION99.63
2.51-2.650.36361550.32442549X-RAY DIFFRACTION99.85
2.65-2.810.31031390.30482586X-RAY DIFFRACTION100
2.81-3.030.38581290.30052606X-RAY DIFFRACTION99.93
3.03-3.330.3011350.2622598X-RAY DIFFRACTION99.93
3.33-3.820.25881400.23282621X-RAY DIFFRACTION99.96
3.82-4.810.24641570.17212620X-RAY DIFFRACTION99.93
4.81-58.250.19831500.18352763X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.72944217844-0.2963666437041.642211160295.21783187691-0.4694395043794.283053822560.03007586642610.6762968475560.774164830202-0.597854477412-0.04213371656260.266923260789-0.2974115406880.2260466789060.1281124539070.5325310430730.05427414991-0.05004715703490.7423176304320.1169809005590.70910601199915.1514145954239.87656864-7.64381527911
20.607185902371-0.5657061471180.644532869043.513109129960.2216987875523.32946769835-0.272696817651.11117773456-0.897801965241-1.655664323420.531279366787-0.9523403329850.3611992778140.7621586671510.009007579417031.048238594830.007392622956880.02547332088141.089211228610.003080383257030.88263543612625.4335929777231.020328746-10.5664473239
32.234361733050.5762555351820.5984114195724.46333672675-1.012103947473.885596228630.1406160369610.09228546566080.297123096918-0.0196866266634-0.167715408391-0.1827119735080.08508011999610.1691844024120.03114315082690.3698918383810.08271929502880.01369002673870.5490294469770.02058980103010.54621740480424.2995311084230.500967598.02463615791
43.68759914668-0.01601060126980.8767161941255.2537512766-0.3458715948434.848626592920.344075092693-0.349654626378-0.1791697830780.2312256043640.01946755205951.035238651631.03231749868-0.724382098648-0.3747824852230.612814999583-0.134700461734-0.01002476479250.6730702811160.04106932886440.5933981356328.68647018405215.20397978812.3869448161
52.154616255870.1704963946291.247142366575.37525354141-0.06785200251473.638647195870.7048760230620.230411332418-0.700390336961-0.254685554024-0.1978445870880.1445165101521.73582747159-0.0106602546777-0.5220263329171.46531550440.11915268253-0.2894841538460.636037157806-0.05322817574370.61664124626521.2413989019201.6157686313.0725783679
61.88572834151-0.1579580265970.5699083147945.67729792826-1.634673628863.347742510650.505208151388-0.329850883635-0.7127412075830.392608576504-0.137555779174-0.324775195621.65186311499-0.0701096599434-0.4291875514911.612996297610.0526143961565-0.3293140445950.6323076053620.02728835119640.66469917203828.1733507362201.30152103317.3326808476
74.42747789841-1.113812669052.153805412150.690360903768-1.633327678064.05513185614-0.18227452183-0.4032893288260.27649213892-0.067679492706-0.06357571832830.205981488120.154681177398-0.6581259909430.2719058901480.798734524076-0.004264461956550.01455349772860.5837155648030.04043586172260.53377934342916.5821478469216.3886231269.6382434424
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 68 )AA7 - 681 - 62
22chain 'A' and (resid 69 through 95 )AA69 - 9563 - 83
33chain 'A' and (resid 96 through 172 )AA96 - 17284 - 160
44chain 'A' and (resid 173 through 278 )AA173 - 278161 - 266
55chain 'A' and (resid 279 through 332 )AA279 - 332267 - 320
66chain 'A' and (resid 333 through 372 )AA333 - 372321 - 360
77chain 'B' and (resid 1 through 6 )BB1 - 61 - 6

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