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- PDB-4hwa: Crystal Structure of Escherichia coli MscS Wildtype (Open State) -

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Basic information

Entry
Database: PDB / ID: 4hwa
TitleCrystal Structure of Escherichia coli MscS Wildtype (Open State)
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / Mechanosensitive Channel / Membrane
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / identical protein binding / membrane / plasma membrane
Similarity search - Function
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, 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 / LSM domain superfamily
Similarity search - Domain/homology
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.37 Å
AuthorsLai, J.Y. / Poon, Y.S. / Kaiser, J. / Rees, D.C.
CitationJournal: Protein Sci. / Year: 2013
Title: Open and shut: crystal structures of the dodecylmaltoside solubilized mechanosensitive channel of small conductance from Escherichia coli and Helicobacter pylori at 4.4 A and 4.1 A resolutions.
Authors: Lai, J.Y. / Poon, Y.S. / Kaiser, J.T. / Rees, D.C.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 area34220 Å2
ΔGint-164 kcal/mol
Surface area82260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.240, 149.970, 175.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
211chain 'B' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
311chain 'C' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
411chain 'D' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
511chain 'E' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
611chain 'F' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )
711chain 'G' and (resseq 25:123 or resseq 125:145 or resseq 147:280 )

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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) / Strain: K12 / Gene: b2924, JW2891, mscS, yggB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris HCl pH 8.5, 30% PEG 400, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011 / Details: K-B Focusing Mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.37→46.576 Å / Num. all: 22481 / Num. obs: 21374 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 4.37→4.48 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1636 / Rsym value: 0.597 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.37→37.914 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 1080 5.05 %
Rwork0.2669 --
all0.268 22481 -
obs0.268 21374 94.81 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.37→37.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13678 0 0 0 13678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613853
X-RAY DIFFRACTIONf_angle_d1.11118788
X-RAY DIFFRACTIONf_dihedral_angle_d16.4655019
X-RAY DIFFRACTIONf_chiral_restr0.0752303
X-RAY DIFFRACTIONf_plane_restr0.0042387
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1937X-RAY DIFFRACTIONPOSITIONAL0.036
12B1937X-RAY DIFFRACTIONPOSITIONAL0.036
13C1937X-RAY DIFFRACTIONPOSITIONAL0.026
14D1937X-RAY DIFFRACTIONPOSITIONAL0.023
15E1937X-RAY DIFFRACTIONPOSITIONAL0.051
16F1937X-RAY DIFFRACTIONPOSITIONAL0.025
17G1937X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.37-4.56860.33051320.29452315X-RAY DIFFRACTION88
4.5686-4.8090.32691410.25762413X-RAY DIFFRACTION92
4.809-5.10970.2831360.2322430X-RAY DIFFRACTION93
5.1097-5.50310.26071420.2392510X-RAY DIFFRACTION95
5.5031-6.05490.30581040.25172547X-RAY DIFFRACTION95
6.0549-6.92640.30591320.25692597X-RAY DIFFRACTION97
6.9264-8.70910.24451410.24682701X-RAY DIFFRACTION100
8.7091-37.91530.29541520.28782781X-RAY DIFFRACTION99

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