[English] 日本語
Yorodumi
- PDB-6z9l: Enterococcal PrgA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z9l
TitleEnterococcal PrgA
Components
  • Poly-alanine peptide
  • PrgA
KeywordsCELL ADHESION / Protease domain / CAP domain / coiled-coil
Function / homologySEC10/PgrA surface exclusion domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / metal ion binding / LPXTG cell wall anchor domain
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.063 Å
AuthorsBerntsson, R.P.A. / Schmitt, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Other privateJCK-1524 Sweden
Other privateSMK-1869 Sweden
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Enterococcal PrgA Extends Far Outside the Cell and Provides Surface Exclusion to Protect against Unwanted Conjugation.
Authors: Schmitt, A. / Hirt, H. / Jarva, M.A. / Sun, W.S. / Ter Beek, J. / Dunny, G.M. / Berntsson, R.P.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PrgA
F: Poly-alanine peptide
G: Poly-alanine peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,91017
Polymers88,5663
Non-polymers1,34514
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-137 kcal/mol
Surface area49570 Å2
Unit cell
Length a, b, c (Å)126.356, 126.356, 293.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein PrgA


Mass: 87250.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgA / Production host: Escherichia coli (E. coli) / References: UniProt: Q04111
#2: Protein/peptide Poly-alanine peptide


Mass: 657.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.62 Å3/Da / Density % sol: 83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 37.5% (v/v) PEG400, 0.1 M Tris/HCl (pH 8.5), 0.114 M LiSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 3.06→49.107 Å / Num. obs: 45500 / % possible obs: 99.5 % / Redundancy: 12.682 % / Biso Wilson estimate: 102.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.266 / Χ2: 1.076 / Net I/σ(I): 8.56 / Num. measured all: 577045
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.06-3.2511.2212.5880.7579085724970480.3422.7197.2
3.25-3.4713.731.741.4593131678467830.5891.807100
3.47-3.7512.8730.912.9581884636163610.8520.949100
3.75-4.113.1050.4526.477322590059000.9680.471100
4.1-4.5812.7620.26810.368239534853470.9860.279100
4.58-5.2812.9580.1813.261760476747660.9950.188100
5.28-6.4512.5920.20912.0451440408540850.9890.218100
6.45-9.0512.6630.09824.6941105324732460.9980.102100
9.05-49.10711.7510.06235.8523079198619640.9980.06598.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z9K

6z9k


Resolution: 3.063→49.107 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3182 2099 4.62 %
Rwork0.2865 43374 -
obs0.2879 45473 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 598.68 Å2 / Biso mean: 134.9054 Å2 / Biso min: 32.99 Å2
Refinement stepCycle: final / Resolution: 3.063→49.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 70 0 5948
Biso mean--166.7 --
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035972
X-RAY DIFFRACTIONf_angle_d0.5768044
X-RAY DIFFRACTIONf_chiral_restr0.033920
X-RAY DIFFRACTIONf_plane_restr0.0021064
X-RAY DIFFRACTIONf_dihedral_angle_d16.7933771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.063-3.13410.40011280.4291265693
3.1341-3.21250.42741380.41622851100
3.2125-3.29930.36921380.39562839100
3.2993-3.39640.33751380.37192869100
3.3964-3.5060.39411390.37152874100
3.506-3.63120.38861380.34852847100
3.6312-3.77660.31741390.31752871100
3.7766-3.94840.31551400.2772886100
3.9484-4.15640.27451380.25622881100
4.1564-4.41670.28981400.24782883100
4.4167-4.75750.30491400.25952902100
4.7575-5.23570.3091420.26432930100
5.2357-5.99220.39891430.31642944100
5.9922-7.54510.31961440.29142984100
7.5451-49.1070.27561540.24163157100

+
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://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