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- PDB-8rtc: Rap from bacteriophage Phi3T in presence of pheromone RGHTS -

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Basic information

Entry
Database: PDB / ID: 8rtc
TitleRap from bacteriophage Phi3T in presence of pheromone RGHTS
Components
  • Pheromone RGHTS
  • 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: 2.83 Å
AuthorsFelipe-Ruiz, A. / Zamora-Caballero, S. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities 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: Rap3T
C: Pheromone RGHTS
D: Pheromone RGHTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7148
Polymers91,1744
Non-polymers3,5404
Water72140
1
A: Rap3T
C: Pheromone RGHTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2425
Polymers45,5872
Non-polymers2,6553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rap3T
D: Pheromone RGHTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4723
Polymers45,5872
Non-polymers8851
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 92.660, 101.970
Angle α, β, γ (deg.)90.000, 107.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999980963689, -0.00172833696955, -0.00592326861513), (0.0017682937714, -0.999975674255, -0.00674715022106), (-0.00591146317804, -0.0067574958592, 0.999959694614)-58.517952766, 31.0029674311, -0.0565943039022
2given(-0.999765427598, -0.011959019255, -0.0180574537954), (0.0116294292681, -0.99976585065, 0.0182482944251), (-0.0182714573587, 0.0180340159971, 0.999670409742)-57.1601121117, 27.9573964211, -0.1941822316

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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 RGHTS


Mass: 558.589 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.: 4 / Source method: obtained synthetically / Formula: C39H80O21
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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 Å3/Da / Density % sol: 59.02 %
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: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.83→97.48 Å / Num. obs: 24531 / % possible obs: 91.48 % / Redundancy: 21.6 % / Biso Wilson estimate: 72.33 Å2 / CC1/2: 0.898 / Net I/σ(I): 23.93
Reflection shellResolution: 2.83→2.931 Å / Num. unique obs: 2392 / CC1/2: 0.574

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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: 2.83→97.48 Å / SU ML: 0.3722 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 1244 5.25 %
Rwork0.228 22444 -
obs0.2301 23688 91.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.53 Å2
Refinement stepCycle: LAST / Resolution: 2.83→97.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 40 40 6017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046100
X-RAY DIFFRACTIONf_angle_d0.77198197
X-RAY DIFFRACTIONf_chiral_restr0.0502868
X-RAY DIFFRACTIONf_plane_restr0.00831038
X-RAY DIFFRACTIONf_dihedral_angle_d15.00772272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.940.30491280.33512514X-RAY DIFFRACTION93.13
2.94-3.080.34651400.30682538X-RAY DIFFRACTION93.18
3.08-3.240.34491240.29372511X-RAY DIFFRACTION92.91
3.24-3.440.3291660.26732486X-RAY DIFFRACTION92.18
3.44-3.710.28091440.24932506X-RAY DIFFRACTION92.24
3.71-4.080.29421460.21682483X-RAY DIFFRACTION91.57
4.08-4.670.26711350.20022469X-RAY DIFFRACTION90.79
4.67-5.890.24381450.20872468X-RAY DIFFRACTION90.57
5.89-97.480.19421160.19822469X-RAY DIFFRACTION87.81
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)
13.35489254518-1.231544074230.4323637745954.17157086970.1400624115911.54825325763-0.1350662256-0.599763595088-0.6544539150180.1420612303050.1282135222630.4909644375310.2543200263490.09420381413-0.2265903181680.7193367526990.0311238092414-0.06299429176290.7415055677940.06717703151560.709947885514-13.7361848553-15.6157021677143.469493766
21.72434293177-1.445429240150.6581318883073.603385835351.30808150322.502313264570.0186349175648-0.230786757944-0.9910076158-0.259258434901-0.2738187573430.2543575754250.871797126267-0.393946060689-0.09935887715340.860365894976-0.0669259984333-0.04577367723850.6424073504890.07237394914740.667252821102-24.8602634914-13.4023988243135.461868485
32.95471499229-0.611933463903-1.455314149272.85879909954-0.2376934145553.138364950990.201017987944-0.1037530062230.188148407297-0.4036910939710.196511479342-0.240145937972-0.3800662719720.324946250141-0.2541444199830.7068361205-0.0712193724754-0.0107668994830.453212520958-0.07248671857230.38418872099-15.42660938784.68538315658129.340356832
42.1671075724-0.616300508189-0.2092132357152.43732491695-0.1109258355771.793385015340.4312601144260.4053571426920.130067884558-1.08507348585-0.317981264628-0.826740608473-0.2072183642030.925457878057-0.174762799581.11692968501-0.03656234751430.1801425823670.752600224565-0.02696870272320.740275662494-6.561270143190.234380220207110.656355584
52.84671967987-0.2714105374020.5490805558883.362456564660.2856048474252.205500128070.7233160216180.467738649164-0.301841831727-1.57976865931-0.5136834485740.217192102468-0.436759146092-0.194765779531-0.1913470867681.994723818460.212168324167-0.1179252768050.608097322924-0.008214173629210.296487208022-22.95875161541.10512445484104.760484456
62.8050430696-2.65894208834-0.7431676329133.7159079207-0.06933891277651.53258480537-0.148024586041-0.1761703708820.486291504997-0.08448835859490.228124688035-0.291562070996-0.53613246040.017884488191-0.2250883858920.643961493149-0.02144950071890.03046842669280.646160833076-0.05623581406430.581836863074-41.606478280944.585870063140.444105535
72.0888576128-0.9135777704530.9096198795323.332874241230.1684648207933.597744223180.3103534151280.0905082463314-0.253861952053-0.836334392408-0.01107056313090.5044721878860.41681935903-0.413765032663-0.1967872231560.739669876549-0.088521360847-0.06150737995510.5019278542670.06550814051790.497998862594-46.295411999326.5847875496124.283602273
82.33796768509-0.810363615855-0.2394590087324.310785133380.7311157252642.315249029030.6742917502050.3193517940420.142024833527-1.61448269078-0.4597902525230.1171732524970.18714488052-0.0383160232495-0.1748639920421.933970909050.232249486577-0.009194651683070.654046808930.03464105195620.361374300524-36.255789055529.3651915615104.794629679
95.47209171546-0.744842527061-2.432923071453.962165109282.726223669332.575849122140.685232898698-0.00365077258796-0.390264671933-0.536761615926-0.290263813123-0.8874424522720.141130863479-0.424233119305-0.2486699416611.16070917184-0.1427385282810.08569104838070.5079671837270.006959105515350.479262848776-14.72290322411.28917078953121.450091728
103.346118694210.08666818401592.906721681834.60044724016-2.082749841283.510116862950.401462402487-0.176589355563-0.643411795188-0.515426904496-0.5084491316220.51446828343-0.293041894032-0.321830029492-0.1773993382630.9355512903350.0723691230818-0.02024595235440.5903192552690.08447063627970.573075258478-44.63357097628.7080443992121.475343469
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 - 60
22chain 'A' and (resid 69 through 112 )AA69 - 11261 - 96
33chain 'A' and (resid 113 through 233 )AA113 - 23397 - 217
44chain 'A' and (resid 234 through 278 )AA234 - 278218 - 262
55chain 'A' and (resid 279 through 371 )AA279 - 371263 - 355
66chain 'B' and (resid 7 through 112 )BB7 - 1121 - 94
77chain 'B' and (resid 113 through 278 )BB113 - 27895 - 260
88chain 'B' and (resid 279 through 371 )BB279 - 371261 - 353
99chain 'C' and (resid 1 through 5 )CC1 - 51 - 5
1010chain 'D' and (resid 1 through 5 )DD1 - 51 - 5

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