[English] 日本語
Yorodumi
- PDB-5xu0: Structure of the membrane fusion protein Spr0693 from Streptococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xu0
TitleStructure of the membrane fusion protein Spr0693 from Streptococcus pneumoniae R6
ComponentsMembrane-fusion protein
KeywordsTRANSPORT PROTEIN / membrane fusion protein / channel
Function / homologyRND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / transmembrane transporter activity / membrane => GO:0016020 / Membrane-fusion protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsYang, H.B. / Jiang, Y.L. / Hou, W.T. / Chen, M.T. / Chen, Y. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology2015CB910103 China
National Natural Science Foundation of China31400628 China
CitationJournal: Nat Commun / Year: 2018
Title: Structure of a MacAB-like efflux pump from Streptococcus pneumoniae.
Authors: Yang, H.B. / Hou, W.T. / Cheng, M.T. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
History
DepositionJun 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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: Membrane-fusion protein
B: Membrane-fusion protein
C: Membrane-fusion protein


Theoretical massNumber of molelcules
Total (without water)87,0703
Polymers87,0703
Non-polymers00
Water0
1
A: Membrane-fusion protein
B: Membrane-fusion protein
C: Membrane-fusion protein

A: Membrane-fusion protein
B: Membrane-fusion protein
C: Membrane-fusion protein


Theoretical massNumber of molelcules
Total (without water)174,1396
Polymers174,1396
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14390 Å2
ΔGint-47 kcal/mol
Surface area70130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.210, 159.210, 99.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Membrane-fusion protein


Mass: 29023.213 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 59-324 / Mutation: T197M, I317M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ERS515107_03100 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Y3EE53

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.22 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 7.5 % PEG 4000, 100 mM CaCl2, 10%-20% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 27463 / % possible obs: 99.8 % / Redundancy: 7 % / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.1 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD
Starting model: 1F3O

1f3o


Resolution: 2.95→48.981 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.87
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.3052 1305 4.75 %
Rwork0.2478 --
obs0.2504 27463 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→48.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 0 0 5102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045142
X-RAY DIFFRACTIONf_angle_d0.7936958
X-RAY DIFFRACTIONf_dihedral_angle_d3.6963137
X-RAY DIFFRACTIONf_chiral_restr0.045814
X-RAY DIFFRACTIONf_plane_restr0.003912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9486-3.06660.45121350.40012844X-RAY DIFFRACTION99
3.0666-3.20610.40961410.36862862X-RAY DIFFRACTION100
3.2061-3.37510.38771350.32172853X-RAY DIFFRACTION100
3.3751-3.58650.34121420.28412871X-RAY DIFFRACTION100
3.5865-3.86330.31961650.26732861X-RAY DIFFRACTION100
3.8633-4.25190.29381430.24712897X-RAY DIFFRACTION100
4.2519-4.86670.25881660.21112888X-RAY DIFFRACTION100
4.8667-6.12970.26541520.24492954X-RAY DIFFRACTION100
6.1297-48.98750.30531260.21063128X-RAY DIFFRACTION100

+
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