[English] 日本語
Yorodumi
- PDB-6aeo: TssL periplasmic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aeo
TitleTssL periplasmic domain
ComponentsMaltose/maltodextrin-binding periplasmic protein,TssL
KeywordsPROTEIN TRANSPORT / structural protein
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / membrane => GO:0016020 / periplasmic space / DNA damage response / membrane
Similarity search - Function
Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
OmpA-like domain-containing protein / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Serratia sp. YD25 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRan, T.T. / Wang, W.W. / Wang, X.B. / Xu, D.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770074 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2018
Title: Crystal structure of the periplasmic domain of TssL, a key membrane component of Type VI secretion system.
Authors: Wang, X. / Sun, B. / Xu, M. / Qiu, S. / Xu, D. / Ran, T. / He, J. / Wang, W.
History
DepositionAug 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,TssL
B: Maltose/maltodextrin-binding periplasmic protein,TssL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5833
Polymers125,4912
Non-polymers921
Water8,179454
1
A: Maltose/maltodextrin-binding periplasmic protein,TssL


Theoretical massNumber of molelcules
Total (without water)62,7461
Polymers62,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24890 Å2
MethodPISA
2
B: Maltose/maltodextrin-binding periplasmic protein,TssL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8382
Polymers62,7461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.353, 108.887, 236.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,TssL / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 62745.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Serratia sp. YD25 (bacteria)
Gene: malE, Z5632, ECs5017, ATE40_012305 / Production host: Escherichia coli (E. coli) / Variant (production host): C43(DE3)
References: UniProt: P0AEY0, UniProt: A0A1B3FDW3, UniProt: P0AEX9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG MME 2000, KSCN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 53257 / % possible obs: 99.7 % / Observed criterion σ(F): 2.8 / Redundancy: 13.3 % / Rpim(I) all: 0.051 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7672 / CC1/2: 0.88 / Rpim(I) all: 0.271 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2287 2705 5.08 %
Rwork0.183 --
obs0.1854 53257 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8451 0 6 454 8911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088651
X-RAY DIFFRACTIONf_angle_d0.91411732
X-RAY DIFFRACTIONf_dihedral_angle_d17.6935225
X-RAY DIFFRACTIONf_chiral_restr0.0491268
X-RAY DIFFRACTIONf_plane_restr0.0061536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34180.30561310.25022602X-RAY DIFFRACTION100
2.3418-2.38690.36071380.23562675X-RAY DIFFRACTION100
2.3869-2.43560.26651270.22572579X-RAY DIFFRACTION100
2.4356-2.48850.30811250.2292649X-RAY DIFFRACTION99
2.4885-2.54640.32731620.22162574X-RAY DIFFRACTION99
2.5464-2.61010.2571380.2082601X-RAY DIFFRACTION100
2.6101-2.68070.28331320.19792698X-RAY DIFFRACTION100
2.6807-2.75950.25161420.20012594X-RAY DIFFRACTION100
2.7595-2.84860.23791430.19832658X-RAY DIFFRACTION100
2.8486-2.95040.26251230.20742644X-RAY DIFFRACTION100
2.9504-3.06850.29141420.21332644X-RAY DIFFRACTION100
3.0685-3.20810.25781480.20842668X-RAY DIFFRACTION100
3.2081-3.37720.26191500.19612602X-RAY DIFFRACTION99
3.3772-3.58870.22191450.17772665X-RAY DIFFRACTION100
3.5887-3.86560.21931580.16752669X-RAY DIFFRACTION100
3.8656-4.25440.17841490.15792688X-RAY DIFFRACTION100
4.2544-4.86940.17631500.14282689X-RAY DIFFRACTION100
4.8694-6.13240.19681410.16822760X-RAY DIFFRACTION100
6.1324-100.18751610.1612893X-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://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