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- PDB-4lku: Structure of the C-terminal domain of the E. coli mechanosensitiv... -

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Basic information

Entry
Database: PDB / ID: 4lku
TitleStructure of the C-terminal domain of the E. coli mechanosensitive channel of large conductance
ComponentsLarge-conductance mechanosensitive channel
KeywordsTRANSPORT PROTEIN / pentamer
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transport / monoatomic ion transmembrane transport / identical protein binding / membrane / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
: / Large-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsWalton, T.A. / Rees, D.C.
CitationJournal: Protein Sci. / Year: 2013
Title: Structure and stability of the C-terminal helical bundle of the E. coli mechanosensitive channel of large conductance.
Authors: Walton, T.A. / Rees, D.C.
History
DepositionJul 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)16,1885
Polymers16,1885
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-27 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.250, 55.120, 32.850
Angle α, β, γ (deg.)90.000, 93.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Large-conductance mechanosensitive channel


Mass: 3237.615 Da / Num. of mol.: 5 / Fragment: UNP residues 108-136 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: C9QXJ2, UniProt: P0A742*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 0.34M ammonium acetate, 34% PEG 2000 MME, 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: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal K-B focusing mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→32.786 Å / Num. all: 19178 / Num. obs: 19178 / % possible obs: 94.2 % / Redundancy: 5.9 % / Rsym value: 0.134 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.535.90.7420.91644527800.74293.5
1.53-1.625.80.5241.41531826480.52494.8
1.62-1.735.30.3881.81280423950.38890.8
1.73-1.8760.2592.71407723410.25996
1.87-2.056.10.1783.61347721930.17896.5
2.05-2.295.80.1484.21139219790.14896.9
2.29-2.655.60.1384.2895615920.13888.2
2.65-3.246.20.1025.9937215120.10298.4
3.24-4.595.60.0925.9615810920.09291.4
4.59-23.7216.70.0954.143366460.09596.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→23.721 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8486 / SU ML: 0.17 / σ(F): 1.36 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 966 5.04 %
Rwork0.1687 --
obs0.1717 19157 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.95 Å2 / Biso mean: 18.602 Å2 / Biso min: 5.39 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 0 136 1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061043
X-RAY DIFFRACTIONf_angle_d1.0221410
X-RAY DIFFRACTIONf_chiral_restr0.048170
X-RAY DIFFRACTIONf_plane_restr0.004192
X-RAY DIFFRACTIONf_dihedral_angle_d13.821431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.52640.23011430.172571271493
1.5264-1.62210.23741400.16242589272994
1.6221-1.74730.23121340.16662467260190
1.7473-1.9230.25021320.15182700283297
1.923-2.20110.21691280.14222684281296
2.2011-2.77250.21961400.17692514265491
2.7725-23.7210.22171490.1822666281595

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