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- PDB-4hw9: Crystal Structure of Helicobacter pylori MscS (Closed State) -

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Basic information

Entry
Database: PDB / ID: 4hw9
TitleCrystal Structure of Helicobacter pylori MscS (Closed State)
ComponentsMechanosensitive channel MscS
KeywordsMEMBRANE PROTEIN / Mechanosensitive Channel / Membrane
Function / homology
Function and homology information


transmembrane transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
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
Mechanosensitive channel MscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.14 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 angstrom and 4.1 angstrom 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 1.1Aug 28, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Mechanosensitive channel MscS
B: Mechanosensitive channel MscS
C: Mechanosensitive channel MscS
D: Mechanosensitive channel MscS
E: Mechanosensitive channel MscS
F: Mechanosensitive channel MscS
G: Mechanosensitive channel MscS


Theoretical massNumber of molelcules
Total (without water)240,7727
Polymers240,7727
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40820 Å2
ΔGint-242 kcal/mol
Surface area83580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.920, 143.100, 178.370
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-IDDetails
11chain A and (resseq 18:235 or resseq 239:270 )
21chain B and (resseq 18:235 or resseq 239:270 )
31chain C and (resseq 18:235 or resseq 239:270 )
41chain D and (resseq 18:235 or resseq 239:270 )
51chain E and (resseq 18:235 or resseq 239:270 )
61chain F and (resseq 18:235 or resseq 239:270 )
71chain G and (resseq 18:235 or resseq 239:270 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLYGLYchain 'A' and (resseq 18:235 or resseq 239:270 )AA18 - 23542 - 259
12VALVALGLNGLNchain 'A' and (resseq 18:235 or resseq 239:270 )AA239 - 270263 - 294
21PHEPHEGLYGLYchain 'B' and (resseq 18:235 or resseq 239:270 )BB18 - 23542 - 259
22VALVALGLNGLNchain 'B' and (resseq 18:235 or resseq 239:270 )BB239 - 270263 - 294
31PHEPHEGLYGLYchain 'C' and (resseq 18:235 or resseq 239:270 )CC18 - 23542 - 259
32VALVALGLNGLNchain 'C' and (resseq 18:235 or resseq 239:270 )CC239 - 270263 - 294
41PHEPHEGLYGLYchain 'D' and (resseq 18:235 or resseq 239:270 )DD18 - 23542 - 259
42VALVALGLNGLNchain 'D' and (resseq 18:235 or resseq 239:270 )DD239 - 270263 - 294
51PHEPHEGLYGLYchain 'E' and (resseq 18:235 or resseq 239:270 )EE18 - 23542 - 259
52VALVALGLNGLNchain 'E' and (resseq 18:235 or resseq 239:270 )EE239 - 270263 - 294
61PHEPHEGLYGLYchain 'F' and (resseq 18:235 or resseq 239:270 )FF18 - 23542 - 259
62VALVALGLNGLNchain 'F' and (resseq 18:235 or resseq 239:270 )FF239 - 270263 - 294
71PHEPHEGLYGLYchain 'G' and (resseq 18:235 or resseq 239:270 )GG18 - 23542 - 259
72VALVALGLNGLNchain 'G' and (resseq 18:235 or resseq 239:270 )GG239 - 270263 - 294

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Components

#1: Protein
Mechanosensitive channel MscS


Mass: 34395.980 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: MscS / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: E8QGV2

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM citrate pH 5.0, 200 mM lithium chloride, 28% PEG 400, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2008 / 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: 1 Å / Relative weight: 1
ReflectionResolution: 4.14→46.081 Å / Num. all: 22495 / Num. obs: 20129 / % possible obs: 89 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 4.14→4.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.755 / % possible all: 98.4

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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: 4.14→44.563 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 37.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 1036 5.15 %
Rwork0.2441 --
obs0.2469 20129 88.23 %
all-22495 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.14→44.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13797 0 0 0 13797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02314007
X-RAY DIFFRACTIONf_angle_d2.76618949
X-RAY DIFFRACTIONf_dihedral_angle_d14.8665075
X-RAY DIFFRACTIONf_chiral_restr0.1452352
X-RAY DIFFRACTIONf_plane_restr0.0162331
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1944X-RAY DIFFRACTIONPOSITIONAL0.11
12B1944X-RAY DIFFRACTIONPOSITIONAL0.11
13C1944X-RAY DIFFRACTIONPOSITIONAL0.118
14D1944X-RAY DIFFRACTIONPOSITIONAL0.107
15E1944X-RAY DIFFRACTIONPOSITIONAL0.116
16F1944X-RAY DIFFRACTIONPOSITIONAL0.118
17G1944X-RAY DIFFRACTIONPOSITIONAL0.107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1401-4.35810.42391230.32182356X-RAY DIFFRACTION78
4.3581-4.63090.31481400.24252507X-RAY DIFFRACTION83
4.6309-4.98810.29751340.20182579X-RAY DIFFRACTION84
4.9881-5.48920.32411530.20372675X-RAY DIFFRACTION87
5.4892-6.28160.32341550.23792804X-RAY DIFFRACTION91
6.2816-7.9070.32281690.24543008X-RAY DIFFRACTION97
7.907-44.56580.27661620.24953164X-RAY DIFFRACTION97

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