[English] 日本語
Yorodumi
- PDB-2oau: Mechanosensitive Channel of Small Conductance (MscS) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oau
TitleMechanosensitive Channel of Small Conductance (MscS)
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / stretch activated / mechanosensitive ion channel
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / membrane / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site ...Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / Alpha-Beta Plaits - #100 / LSM domain superfamily / SH3 type barrels. / Helix Hairpins / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsRees, D.C. / Bass, R.B. / Steinbacher, S. / Strop, P. / Barclay, M.T.
Citation
Journal: CURRENT TOPICS IN MEMBRANES / Year: 2007
Title: Structures of the Prokaryotic Mechanosensitive Channels MscL and MscS
Authors: Steinbacher, S. / Bass, R. / Strop, P. / Rees, D.C.
#1: Journal: Science / Year: 2002
Title: The crystal structure of E. coli MscS, a voltage-modulated and mechanosensitive channel
Authors: Bass, R.B. / Strop, P. / Barclay, M. / Rees, D.C.
History
DepositionDec 17, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionJan 9, 2007ID: 1MXM
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE ALL THE NON-HISTIDINE RESIDUES IN THE N-TERMINAL 20 RESIDUES ARE PART OF A CLEAVABLE HIS- ...SEQUENCE ALL THE NON-HISTIDINE RESIDUES IN THE N-TERMINAL 20 RESIDUES ARE PART OF A CLEAVABLE HIS-TAG CONSTRUCT THAT WAS ADDED TO THE MSCS SEQUENCE. THE PROTEIN SEQUENCE IS NOT CLEAVED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small-conductance mechanosensitive channel
B: Small-conductance mechanosensitive channel
C: Small-conductance mechanosensitive channel
D: Small-conductance mechanosensitive channel
E: Small-conductance mechanosensitive channel
F: Small-conductance mechanosensitive channel
G: Small-conductance mechanosensitive channel


Theoretical massNumber of molelcules
Total (without water)231,6607
Polymers231,6607
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37600 Å2
ΔGint-227 kcal/mol
Surface area81710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.274, 184.274, 260.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains one heptamer which is the biological unit

-
Components

#1: Protein
Small-conductance mechanosensitive channel


Mass: 33094.258 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mscS / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C0S1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3350, AMMONIUM CHLORIDE, CITRATE, FOSHOLINE-14, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9788, 0.9791, 0.9184, 1.009
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97911
30.91841
41.0091
ReflectionResolution: 3.7→50 Å / Num. obs: 48452 / % possible obs: 100 % / Redundancy: 8.1 % / Rsym value: 0.107 / Net I/σ(I): 20.7
Reflection shellResolution: 3.7→3.81 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2 / Num. unique all: 3962 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1MXM

1mxm
PDB Unreleased entry


Resolution: 3.7→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.321 2429 5 %
Rwork0.293 --
obs-48458 99.9 %
Solvent computationBsol: 45 Å2 / ksol: 0.23 e/Å3
Displacement parametersBiso mean: 117.936 Å2
Baniso -1Baniso -2Baniso -3
1--7.188 Å20 Å20 Å2
2---7.188 Å20 Å2
3---14.376 Å2
Refinement stepCycle: LAST / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13580 0 0 0 13580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.636
X-RAY DIFFRACTIONc_mcbond_it2.231.5
X-RAY DIFFRACTIONc_scbond_it2.9512
X-RAY DIFFRACTIONc_mcangle_it3.9242
X-RAY DIFFRACTIONc_scangle_it4.9482.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
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