[English] 日本語
Yorodumi
- PDB-8rsu: Rap from bacteriophage Phi3T in presence of pheromone RRGHTA -

+
Open data


ID or keywords:

Loading...

-
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 / cytoplasm / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more