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- PDB-2oau: Mechanosensitive Channel of Small Conductance (MscS) -

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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 / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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