[English] 日本語
Yorodumi
- PDB-9g9p: Lipid III flippase WzxE with NB10 and NB7 nanobodies in inward-fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g9p
TitleLipid III flippase WzxE with NB10 and NB7 nanobodies in inward-facing conformation - crystal 2
Components
  • Lipid III flippase
  • NB10 Nanobody
  • NB7 Nanobody
KeywordsTRANSPORT PROTEIN / membrane protein / flippase / cell wall / enterobacterial common antigen
Function / homologyintramembrane lipid transporter activity / Polysaccharide biosynthesis protein / Lipid III flippase WzxE, Proteobacteria / Lipid III flippase WzxE / : / Polysaccharide biosynthesis protein / enterobacterial common antigen biosynthetic process / plasma membrane / Lipid III flippase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLe Bas, A. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Open Biology / Year: 2025
Title: Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide.
Authors: Le Bas, A. / Clarke, B.R. / Teelucksingh, T. / Lee, M. / El Omari, K. / Giltrap, A.M. / McMahon, S.A. / Liu, H. / Beale, J.H. / Mykhaylyk, V. / Duman, R. / Paterson, N.G. / Ward, P.N. / ...Authors: Le Bas, A. / Clarke, B.R. / Teelucksingh, T. / Lee, M. / El Omari, K. / Giltrap, A.M. / McMahon, S.A. / Liu, H. / Beale, J.H. / Mykhaylyk, V. / Duman, R. / Paterson, N.G. / Ward, P.N. / Harrison, P.J. / Weckener, M. / Pardon, E. / Steyaert, J. / Liu, H. / Quigley, A. / Davis, B.G. / Wagner, A. / Whitfield, C. / Naismith, J.H.
History
DepositionJul 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipid III flippase
B: NB10 Nanobody
C: NB7 Nanobody


Theoretical massNumber of molelcules
Total (without water)76,4873
Polymers76,4873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.884, 191.681, 102.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Lipid III flippase


Mass: 46130.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wzxE, wzx, yifJ, b3792, JW3766 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AAA7
#2: Antibody NB10 Nanobody


Mass: 15132.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): wk6 su-
#3: Antibody NB7 Nanobody


Mass: 15223.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): wk6 su-
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 3.8
Details: ammonium sulfate, glycine, triethylene glycol, E. coli polar lipids, monoolein

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 2.8→36.02 Å / Num. obs: 20557 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 980 / CC1/2: 0.8 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34.94 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 1008 4.92 %
Rwork0.22 --
obs0.2226 20501 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 0 0 5045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025162
X-RAY DIFFRACTIONf_angle_d0.4477017
X-RAY DIFFRACTIONf_dihedral_angle_d3.672723
X-RAY DIFFRACTIONf_chiral_restr0.036801
X-RAY DIFFRACTIONf_plane_restr0.003869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.33551490.27332690X-RAY DIFFRACTION99
2.95-3.140.33011460.25272743X-RAY DIFFRACTION100
3.14-3.380.34121350.23612775X-RAY DIFFRACTION100
3.38-3.720.29391540.22372741X-RAY DIFFRACTION100
3.72-4.260.25911270.19622818X-RAY DIFFRACTION100
4.26-5.360.23811410.2112803X-RAY DIFFRACTION100
5.36-34.940.24321560.21182923X-RAY DIFFRACTION100
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)
13.34552.25481.04244.339-0.5222.89640.0074-0.0183-0.33130.4383-0.0752-0.24860.29190.07230.08420.75580.1274-0.00390.32770.02990.340324.4488-39.432839.4692
20.53030.1322-0.10010.2587-0.23011.09130.0097-0.04690.12270.1197-0.0039-0.0444-0.11050.0961-0.00780.562-0.00860.02720.2012-0.00790.41220.15941.951725.0286
31.6433-1.3723-0.61231.67190.89752.0403-0.0930.0535-0.0110.12130.159-0.21460.4583-0.0697-0.05510.75770.0218-0.0040.2416-0.01980.434518.1543-34.442310.6718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 4 through 124)
2X-RAY DIFFRACTION2(chain 'A' and resid 7 through 414)
3X-RAY DIFFRACTION3(chain 'B' and resid 3 through 128)

+
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