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- PDB-8rte: Rap from bacteriophage Phi105 with peptide ERPVGT -

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Basic information

Entry
Database: PDB / ID: 8rte
TitleRap from bacteriophage Phi105 with peptide ERPVGT
Components
  • Peptide ERPVGT
  • Rap105
KeywordsSIGNALING PROTEIN / Rap / Aspartate phosphatase / Phi3T / Bacteriophage
Function / homologyresponse regulator aspartate phosphatase H, N terminal / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi105 (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: Rap105
B: Rap105
D: Peptide ERPVGT
E: Peptide ERPVGT


Theoretical massNumber of molelcules
Total (without water)89,5364
Polymers89,5364
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-22 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 80.307, 91.707
Angle α, β, γ (deg.)90.000, 100.680, 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

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Components

#1: Protein Rap105


Mass: 44109.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi105 (virus) / Gene: PHI105_00140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6R410
#2: Protein/peptide Peptide ERPVGT


Mass: 658.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus phage phi105 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% glycerol ethoxylate, 10% tetrahydrofuran and 0.1M tris-HCl pH8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→90.12 Å / Num. obs: 36368 / % possible obs: 99.37 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.85 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.73
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 3628 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→90.12 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 25.4944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1781 4.9 %
Rwork0.2187 34583 -
obs0.2205 36364 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→90.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5831 0 0 89 5920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00375966
X-RAY DIFFRACTIONf_angle_d0.64548042
X-RAY DIFFRACTIONf_chiral_restr0.0395868
X-RAY DIFFRACTIONf_plane_restr0.00471015
X-RAY DIFFRACTIONf_dihedral_angle_d14.95122213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31271340.28682629X-RAY DIFFRACTION99.32
2.46-2.540.29591480.2722665X-RAY DIFFRACTION99.75
2.54-2.620.30881300.26362641X-RAY DIFFRACTION99.68
2.62-2.710.31341200.25842694X-RAY DIFFRACTION99.68
2.71-2.820.31491270.24922649X-RAY DIFFRACTION99.78
2.82-2.950.26841510.24162648X-RAY DIFFRACTION99.71
2.95-3.110.3051590.24192645X-RAY DIFFRACTION99.89
3.11-3.30.26481400.23892659X-RAY DIFFRACTION99.64
3.3-3.550.25121330.21672643X-RAY DIFFRACTION98.97
3.56-3.910.26151330.19652633X-RAY DIFFRACTION98.26
3.91-4.480.21051500.17762643X-RAY DIFFRACTION98.73
4.48-5.640.22681150.19512691X-RAY DIFFRACTION99.01
5.64-90.120.21461410.20142743X-RAY DIFFRACTION99.28
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)
11.540305386630.166168775025-0.03206841331461.40187989558-0.5455445877191.96578562472-0.04955689756970.315941593977-0.1628073174-0.426447156979-0.15858153424-0.2036767990510.2772059364530.3914107626790.01023897555060.3581532245230.08481104249740.0802085551040.2961792375840.02591577596660.280603220618.50008705737-4.1099426097934.1502482665
20.971496300258-0.147863038980.3910331007621.69315666891-0.9053861077821.37200802839-0.0893986810104-0.01544700591790.09906908753770.02402621459690.08064219128410.0813262123894-0.0477303789316-0.0472185874852-0.009180970760940.188214732850.0112425360449-0.003230303737470.138754363501-0.007914101035260.202960534728-9.79455953198.8297307056243.0557522497
31.226753866010.170373356454-0.1173590699861.35577090781-0.1761978727072.195928835520.0221951373848-0.0463777921821-0.0741893058417-0.1137282895920.08817644013180.07492553849610.104728153033-0.15577248062-0.09262350336470.1795729147950.012946635531-0.01330582295920.1806387415330.02343733384860.176652550875-17.8386186686-9.4175327324952.57239612
41.74457746476-0.2145807423540.7144878019721.615411258590.8095948814391.5348323478-0.0309309341181-0.3380447289590.2505289542410.2862137891390.131519948903-0.143238211084-0.2242955714040.3010214436740.07933667225030.345516487121-0.0409689194334-0.01940812569460.379342855505-0.09883266501310.33445544800425.4278449237-0.42858230435481.439357206
51.53689209673-0.09631184790390.2460918691781.062884958960.1675290298130.6508764037740.0191798955766-0.04877947299740.13090032622-0.0834933648308-0.0220898834006-0.232282572697-0.1254462442320.05918877852760.02812089648020.192754322570.00501007891111-0.004438534081960.1877244180330.01169702288280.23204032674517.5630860388-6.5182689731165.4495424058
62.038539515130.0516789698280.2470279676510.819318488722-0.4783823690040.871999132109-0.0146230842936-0.225193060844-0.135247837150.1414773744240.0390870545670.08605310207980.00756610235608-0.122296690638-0.05919946190810.2128961322710.00375936063221-0.007951001146760.2284139726050.002561197044650.175343539606-0.841679735769-17.441099446776.461292129
70.2560834682290.4507078440.518999841343.1213136137-1.87770592084.368244592310.06370054372920.0425551437908-0.0672163406518-0.305893370670.198113989341-0.163998798438-0.0008991342580140.425242964550.05370587064360.2944587997090.0259238434948-0.03371746937550.2146235406140.03397647542840.230921007872-4.738941978720.94285024540944.2520844853
82.16600156628-1.92115443831.507283583241.93726465905-0.5012251286093.99007225195-0.0627740437174-0.3373321006280.05273428794970.258095772794-0.179926011364-0.0993913053625-0.03117598019440.00205564176967-0.01054842738550.274247889240.0193316962405-0.03439132592230.2195852815070.004405871233040.1726311623528.21424502912-12.853970597973.1485618136
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 165 )AA9 - 1651 - 145
22chain 'A' and (resid 166 through 286 )AA166 - 286146 - 266
33chain 'A' and (resid 287 through 370 )AA287 - 370267 - 350
44chain 'B' and (resid 10 through 106 )BB10 - 1061 - 91
55chain 'B' and (resid 107 through 188 )BB107 - 18892 - 173
66chain 'B' and (resid 189 through 367 )BB189 - 367174 - 350
77chain 'D' and (resid 601 through 606 )DD601 - 6061 - 6
88chain 'E' and (resid 501 through 506 )EE501 - 5061 - 6

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