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- PDB-3hzq: Structure of a tetrameric MscL in an expanded intermediate state -

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Basic information

Entry
Database: PDB / ID: 3hzq
TitleStructure of a tetrameric MscL in an expanded intermediate state
ComponentsLarge-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / intermediate state Mechanosensitive channel osmoregulation / Cell membrane / Ion transport / Ionic channel / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large-conductance mechanosensitive channel
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MW2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.82 Å
AuthorsLiu, Z.F. / Gandhi, C.S. / Rees, D.C.
CitationJournal: Nature / Year: 2009
Title: Structure of a tetrameric MscL in an expanded intermediate state.
Authors: Liu, Z. / Gandhi, C.S. / Rees, D.C.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large-conductance mechanosensitive channel


Theoretical massNumber of molelcules
Total (without water)12,7771
Polymers12,7771
Non-polymers00
Water00
1
A: Large-conductance mechanosensitive channel

A: Large-conductance mechanosensitive channel

A: Large-conductance mechanosensitive channel

A: Large-conductance mechanosensitive channel


Theoretical massNumber of molelcules
Total (without water)51,1094
Polymers51,1094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area8240 Å2
ΔGint-89 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.589, 138.589, 138.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Large-conductance mechanosensitive channel


Mass: 12777.226 Da / Num. of mol.: 1 / Fragment: residue 1-94 / Mutation: S32C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MW2 (bacteria)
Gene: mscL / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold (DE3) / References: UniProt: P68806

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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: 4.34 Å3/Da / Density % sol: 71.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24-30% PEG400, 100 mM Tris-HCl (pH7.0), 150 mM Na2SO4, 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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 2409 / Num. obs: 2395 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.8
Reflection shellResolution: 3.8→3.89 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.82→40.01 Å / Rfactor Rfree error: 0.021 / Data cutoff high absF: 821326.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.312 221 10 %RANDOM
Rwork0.292 ---
obs0.292 2211 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 169.153 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 246.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.09 Å0.8 Å
Luzzati d res low-8 Å
Luzzati sigma a0.56 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.82→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 0 0 748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.447 29 9.3 %
Rwork0.407 282 -
obs--78.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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