[English] 日本語
Yorodumi
- PDB-7zao: Structure of BPP43_05035 of Brachyspira pilosicoli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zao
TitleStructure of BPP43_05035 of Brachyspira pilosicoli
ComponentsSialidase (Neuraminidase) family protein-like protein
KeywordsMEMBRANE PROTEIN / bacterial membrane protein / adhesion-molecule
Function / homologySialidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Sialidase (Neuraminidase) family protein-like protein
Function and homology information
Biological speciesBrachyspira pilosicoli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRajan, A. / Gallego, P. / Pelaseyed, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Wenner-Gren Foundation United States
CitationJournal: Biorxiv / Year: 2024
Title: BPP43_05035 is a Brachyspira pilosicoli cell surface adhesin that weakens the integrity of the epithelial barrier during infection
Authors: Rajan, A. / Gallego, P. / Dolan, B. / Patel, P. / Dwibedi, C. / Luis, A.S. / Trillo-Muyo, S. / Arike, L. / van der Post, S. / Simren, M. / Pelaseyed, T.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sialidase (Neuraminidase) family protein-like protein
B: Sialidase (Neuraminidase) family protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6166
Polymers98,5182
Non-polymers974
Water5,368298
1
A: Sialidase (Neuraminidase) family protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3083
Polymers49,2591
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase (Neuraminidase) family protein-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3083
Polymers49,2591
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.907, 101.358, 154.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 26 through 188 or resid 190 through 454 or resid 501 through 502))
d_2ens_1(chain "B" and (resid 26 through 188 or resid 190 through 454 or resid 501 through 502))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNILEILEAA26 - 18826 - 188
d_12TRPTRPTYRTYRAA190 - 454190 - 454
d_13MGMGMGMGAC - D501 - 502
d_21ASNASNILEILEBB26 - 18826 - 188
d_22TRPTRPTYRTYRBB190 - 454190 - 454
d_23MGMGMGMGBE - F501 - 502

-
Components

#1: Protein Sialidase (Neuraminidase) family protein-like protein


Mass: 49259.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachyspira pilosicoli (bacteria) / Gene: BPP43_05035 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6VYW6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.1 M magnesium chloride, 0.1 M Bis-Tris buffer pH 5.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→48.17 Å / Num. obs: 60457 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.46 Å2 / CC1/2: 0.984 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.549 / Num. unique obs: 740 / CC1/2: 0.528

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.17 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 3033 5.02 %
Rwork0.1827 57378 -
obs0.1847 60411 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 4 298 6716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936554
X-RAY DIFFRACTIONf_angle_d1.16928876
X-RAY DIFFRACTIONf_chiral_restr0.0701972
X-RAY DIFFRACTIONf_plane_restr0.00751170
X-RAY DIFFRACTIONf_dihedral_angle_d6.7519918
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.517600270139 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.35271170.29072385X-RAY DIFFRACTION89.97
2.23-2.270.32371330.28672479X-RAY DIFFRACTION93.35
2.27-2.310.35121390.25852577X-RAY DIFFRACTION96.86
2.31-2.350.30881280.23982589X-RAY DIFFRACTION98.48
2.35-2.40.32011350.22742654X-RAY DIFFRACTION99.15
2.4-2.450.27021370.22512613X-RAY DIFFRACTION99.06
2.45-2.50.25271450.21192628X-RAY DIFFRACTION98.65
2.5-2.560.27241230.21862631X-RAY DIFFRACTION98.78
2.56-2.620.27191420.21092631X-RAY DIFFRACTION98.89
2.62-2.690.27271380.21432616X-RAY DIFFRACTION98.53
2.69-2.770.28891420.22442629X-RAY DIFFRACTION98.05
2.77-2.860.26691290.21922635X-RAY DIFFRACTION98.19
2.86-2.960.24391280.20432637X-RAY DIFFRACTION97.95
2.96-3.080.26511440.20282604X-RAY DIFFRACTION97.65
3.08-3.220.22471510.19242596X-RAY DIFFRACTION97.86
3.22-3.390.23551270.19472645X-RAY DIFFRACTION97.81
3.39-3.60.21451620.18352620X-RAY DIFFRACTION97.65
3.6-3.880.21181590.15782591X-RAY DIFFRACTION96.69
3.88-4.270.1621410.14562619X-RAY DIFFRACTION96.44
4.27-4.890.13731220.12032637X-RAY DIFFRACTION96.17
4.89-6.160.15951570.13382626X-RAY DIFFRACTION95.5
6.16-48.170.19421340.15752736X-RAY DIFFRACTION93.82

+
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