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- PDB-4y7j: Structure of an archaeal mechanosensitive channel in expanded state -

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Basic information

Entry
Database: PDB / ID: 4y7j
TitleStructure of an archaeal mechanosensitive channel in expanded state
ComponentsLarge conductance mechanosensitive channel protein,Riboflavin synthase
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / mechanosensitive channel / mechanosensation
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin synthase complex / mechanosensitive monoatomic ion channel activity / riboflavin biosynthetic process / monoatomic ion transport / membrane
Similarity search - Function
Riboflavin synthase, archaeal / Large-conductance mechanosensitive channel MscL / Large-conductance mechanosensitive channel/anditomin synthesis protein L / Large-conductance mechanosensitive channel, MscL / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Domain/homology
Riboflavin synthase / Large conductance mechanosensitive channel protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
Methanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsLi, J. / Liu, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020302 China
Ministry of Science and Technology (China)2014CB910301 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Mechanical coupling of the multiple structural elements of the large-conductance mechanosensitive channel during expansion
Authors: Li, J. / Guo, J. / Ou, X. / Zhang, M. / Li, Y. / Liu, Z.
History
DepositionFeb 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large conductance mechanosensitive channel protein,Riboflavin synthase
B: Large conductance mechanosensitive channel protein,Riboflavin synthase
C: Large conductance mechanosensitive channel protein,Riboflavin synthase
D: Large conductance mechanosensitive channel protein,Riboflavin synthase
E: Large conductance mechanosensitive channel protein,Riboflavin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6536
Polymers154,3475
Non-polymers3061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22070 Å2
ΔGint-200 kcal/mol
Surface area60710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.360, 149.250, 99.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 241
2010B4 - 241
1020A4 - 243
2020C4 - 243
1030A4 - 242
2030D4 - 242
1040A4 - 243
2040E4 - 243
1050B4 - 241
2050C4 - 241
1060B4 - 241
2060D4 - 241
1070B4 - 241
2070E4 - 241
1080C4 - 242
2080D4 - 242
1090C4 - 248
2090E4 - 248
10100D4 - 242
20100E4 - 242

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Large conductance mechanosensitive channel protein,Riboflavin synthase / MscL


Mass: 30869.348 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: chimera of Large conductance mechanosensitive channel protein and Riboflavin synthase
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea), (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: C2A, DSM 2661 / Gene: MA_2285, ribC, MJ1184 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8TNK0, UniProt: Q58584
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.6M (NH4)2SO4, 0.1M NaCl, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→40 Å / Num. obs: 17722 / % possible obs: 99.7 % / Redundancy: 9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.7
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 9 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B98

2b98


Resolution: 4.1→40 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.889 / SU B: 83.545 / SU ML: 1.109 / Cross valid method: THROUGHOUT / ESU R Free: 1.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.37582 898 5.1 %RANDOM
Rwork0.32073 ---
obs0.32335 16770 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 254.683 Å2
Baniso -1Baniso -2Baniso -3
1--8.01 Å20 Å2-0 Å2
2---10.67 Å2-0 Å2
3---18.69 Å2
Refinement stepCycle: LAST / Resolution: 4.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8872 0 21 0 8893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.98312234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.03851156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.48325.26308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.783151623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6741514
X-RAY DIFFRACTIONr_chiral_restr0.1370.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216446
X-RAY DIFFRACTIONr_gen_planes_other
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_it14.14926.584662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it23.79239.7535804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it13.9628.424392
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined44.09738332
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4260.32
12B4260.32
21A4220.34
22C4220.34
31A4160.34
32D4160.34
41A4140.32
42E4140.32
51B4360.32
52C4360.32
61B4480.29
62D4480.29
71B4140.36
72E4140.36
81C4600.3
82D4600.3
91C4500.32
92E4500.32
101D4180.31
102E4180.31
LS refinement shellResolution: 4.1→4.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 66 -
Rwork0.455 1220 -
obs--99.92 %

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