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- PDB-2oar: Mechanosensitive Channel of Large Conductance (MscL) -

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Basic information

Entry
Database: PDB / ID: 2oar
TitleMechanosensitive Channel of Large Conductance (MscL)
ComponentsLarge-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / stretch activated ion channel mechanosensitive
Function / homology
Function and homology information


gated channel activity / intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / plasma membrane => GO:0005886 / monoatomic ion transport / transmembrane transport / membrane => GO:0016020 / identical protein binding / plasma membrane
Similarity search - Function
Large-conductance mechanosensitive channel, MscL; domain 1 / Large-conductance mechanosensitive channel / Large-conductance mechanosensitive channel, conserved site / Large-conductance mechanosensitive channels mscL family signature. / Large-conductance mechanosensitive channel MscL / Large-conductance mechanosensitive channel/anditomin synthesis protein L / Large-conductance mechanosensitive channel, MscL / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Large-conductance mechanosensitive channel, MscL; domain 1 / Large-conductance mechanosensitive channel / Large-conductance mechanosensitive channel, conserved site / Large-conductance mechanosensitive channels mscL family signature. / Large-conductance mechanosensitive channel MscL / Large-conductance mechanosensitive channel/anditomin synthesis protein L / Large-conductance mechanosensitive channel, MscL / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Large-conductance mechanosensitive channel / Large-conductance mechanosensitive channel
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsRees, D.C. / Chang, G. / Spencer, R.H. / Lee, A.T. / Steinbacher, S. / Strop, P.
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: 1998
Title: Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel
Authors: Chang, G. / Spencer, R.H. / Lee, A.T. / Barclay, M.T. / Rees, D.C.
#2: Journal: METHODS AND RESULTS IN CRYSTALLIZATION OF MEMBRANE PROTEINS
Year: 2003
Title: Crystallization and structure determination of MSCL, a gated prokaryotic mechanosensitive channel
History
DepositionDec 17, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionJan 9, 2007ID: 1MSL
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 1.3Apr 9, 2014Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE All the non-histidine residues in the N-terminal 22 residues are part of a cleavable his- ...SEQUENCE All the non-histidine residues in the N-terminal 22 residues are part of a cleavable his-tag construct that was added to the MscL 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: Large-conductance mechanosensitive channel
B: Large-conductance mechanosensitive channel
C: Large-conductance mechanosensitive channel
D: Large-conductance mechanosensitive channel
E: Large-conductance mechanosensitive channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6778
Polymers94,0875
Non-polymers5913
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22150 Å2
ΔGint-197 kcal/mol
Surface area32680 Å2
MethodPISA
2
A: Large-conductance mechanosensitive channel
B: Large-conductance mechanosensitive channel
C: Large-conductance mechanosensitive channel
D: Large-conductance mechanosensitive channel
E: Large-conductance mechanosensitive channel
hetero molecules

A: Large-conductance mechanosensitive channel
B: Large-conductance mechanosensitive channel
C: Large-conductance mechanosensitive channel
D: Large-conductance mechanosensitive channel
E: Large-conductance mechanosensitive channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,35516
Polymers188,17310
Non-polymers1,1826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area47700 Å2
ΔGint-437 kcal/mol
Surface area62540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.308, 212.308, 97.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-600-

AU

DetailsThe asymmetric unit contains one pentamer which is the biological unit

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Components

#1: Protein
Large-conductance mechanosensitive channel /


Mass: 18817.307 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RA / Gene: mscL / Plasmid: pET19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A5K8, UniProt: A5U127*PLUS
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au

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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: 5.9 Å3/Da / Density % sol: 78.97 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 3.7
Details: PROTEIN CONCENTRATION 15-20 MG/ML AND 0.05% DODECYLMALTOSIDE.PROTEIN WAS MIXED IN A RATIO OF 4:3 OR 3:2 WITH THE RESERVOIR SOLUTION CONTAINING 100-120 mM AMMONIUM SULFUATE, 23-27% ...Details: PROTEIN CONCENTRATION 15-20 MG/ML AND 0.05% DODECYLMALTOSIDE.PROTEIN WAS MIXED IN A RATIO OF 4:3 OR 3:2 WITH THE RESERVOIR SOLUTION CONTAINING 100-120 mM AMMONIUM SULFUATE, 23-27% TRIETHYLENE GLYCOL, 100 mM GLYCINE, WITH 1-3 mM GD(CL)3 OR SM(CL)3 AND D2O AS THE SOLVENT. 1 mM (NA3)AU(S2O3)2 WAS SOAKED INTO THE CRYSTAL, pH 3.7, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 25597 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.103 / Net I/σ(I): 12.6
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.458 / % possible all: 50.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.5→20 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.338 1234 4.5 %
Rwork0.319 --
obs0.319 25558 93.2 %
Solvent computationBsol: 40 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 135.31 Å2
Baniso -1Baniso -2Baniso -3
1-21.25 Å20 Å20 Å2
2--21.25 Å20 Å2
3----42.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4755 0 3 0 4758
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.5291.5
X-RAY DIFFRACTIONc_mcangle_it4.6562
X-RAY DIFFRACTIONc_scbond_it2.4232
X-RAY DIFFRACTIONc_scangle_it4.3712.5
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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