[English] 日本語
Yorodumi
- PDB-8c27: Domain 3 of Group B Streptococcus pilus protein as scaffold for t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c27
TitleDomain 3 of Group B Streptococcus pilus protein as scaffold for the display of foreign epitopes
ComponentsPI-2a backbone protein
KeywordsMEMBRANE PROTEIN / Pilus protein / scaffold / epitopes.
Function / homology
Function and homology information


Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
PI-2a backbone protein
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsVeggi, D. / Cappelli, L. / Cozzi, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Domain 3 of Group B Streptococcus pilus protein as scaffold for the display of foreign epitope
Authors: Veggi, D. / Cappelli, L. / Cozzi, R.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PI-2a backbone protein
B: PI-2a backbone protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4574
Polymers29,3332
Non-polymers1242
Water1086
1
A: PI-2a backbone protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7903
Polymers14,6661
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PI-2a backbone protein


Theoretical massNumber of molelcules
Total (without water)14,6661
Polymers14,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.391, 118.047, 189.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

-
Components

#1: Protein PI-2a backbone protein


Mass: 14666.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B9UR22
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES with 20% w/v jeff ED-2001 pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.63→94.9 Å / Num. obs: 12062 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 2.63→94.9 Å / Num. unique obs: 12062 / CC1/2: 0.998

-
Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XTL

2xtl


Resolution: 2.63→58.15 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 598 4.96 %
Rwork0.2266 11459 -
obs0.2292 12057 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.1 Å2
Refinement stepCycle: LAST / Resolution: 2.63→58.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 8 7 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052055
X-RAY DIFFRACTIONf_angle_d1.8222785
X-RAY DIFFRACTIONf_chiral_restr0.0927315
X-RAY DIFFRACTIONf_plane_restr0.0198357
X-RAY DIFFRACTIONf_dihedral_angle_d16.3209751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.90.37971480.32512822X-RAY DIFFRACTION99.76
2.9-3.320.35141580.28142818X-RAY DIFFRACTION99.53
3.32-4.180.27311460.21652863X-RAY DIFFRACTION99.87
4.18-58.150.23161460.1962956X-RAY DIFFRACTION99.45

+
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