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- PDB-4agf: MTSSL spin labeled L124C mutant of MscS in the open form -

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Basic information

Entry
Database: PDB / ID: 4agf
TitleMTSSL spin labeled L124C mutant of MscS in the open form
ComponentsSMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / plasma membrane
Similarity search - Function
Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / 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 ...Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / 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 / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsPliotas, C. / Brannigan, E. / Naismith, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Conformational State of the Mscs Mechanosensitive Channel in Solution Revealed by Pulsed Electron-Electron Double Resonance (Peldor) Spectroscopy.
Authors: Pliotas, C. / Ward, R. / Branigan, E. / Rasmussen, A. / Hagelueken, G. / Huang, H. / Black, S.S. / Booth, I.R. / Schiemann, O. / Naismith, J.H.
History
DepositionJan 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references / Other
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)216,3907
Polymers216,3907
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33570 Å2
ΔGint-184.7 kcal/mol
Surface area86440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.840, 150.220, 175.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL / MSCS


Mass: 30912.887 Da / Num. of mol.: 7 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS SPIN LABELED ON L124C / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C0S2, UniProt: P0C0S1*PLUS
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN B, LEU 124 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN B, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN C, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN D, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN E, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN F, LEU 124 TO CYS ENGINEERED RESIDUE IN CHAIN G, LEU 124 TO CYS
Sequence detailsMUTATION AT L124C

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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: 3.92 Å3/Da / Density % sol: 72.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 4.7→113 Å / Num. obs: 17429 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.8
Reflection shellResolution: 4.7→4.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VV5

2vv5


Resolution: 4.7→114.21 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.854 / SU B: 127.191 / SU ML: 1.424 / Cross valid method: THROUGHOUT / ESU R Free: 1.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY REFINED USED JELLY BODY, NCS LOCAL RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.33923 885 5.1 %RANDOM
Rwork0.33417 ---
obs0.33441 16506 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.713 Å2
Baniso -1Baniso -2Baniso -3
1-11.87 Å20 Å20 Å2
2---12.33 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 4.7→114.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13663 0 0 0 13663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913853
X-RAY DIFFRACTIONr_bond_other_d0.0060.029226
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.96218788
X-RAY DIFFRACTIONr_angle_other_deg3.169322456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23451785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23123.125560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.978152401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.15815126
X-RAY DIFFRACTIONr_chiral_restr0.0680.22303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215407
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022891
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.7→4.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 55 -
Rwork0.413 1083 -
obs--92.75 %

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