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- PDB-4y7k: Structure of an archaeal mechanosensitive channel in closed state -

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Basic information

Entry
Database: PDB / ID: 4y7k
TitleStructure of an archaeal mechanosensitive channel in closed 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: 3.5 Å
AuthorsLi, J. / Liu, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020302 China
Ministry of Science and Technology2014CB910301 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)153,0455
Polymers153,0455
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26240 Å2
ΔGint-246 kcal/mol
Surface area52830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.292, 140.368, 182.544
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
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
1010A3 - 244
2010B3 - 244
1020A3 - 242
2020C3 - 242
1030A3 - 244
2030D3 - 244
1040A3 - 243
2040E3 - 243
1050B3 - 242
2050C3 - 242
1060B3 - 244
2060D3 - 244
1070B3 - 243
2070E3 - 243
1080C3 - 242
2080D3 - 242
1090C3 - 242
2090E3 - 242
10100D3 - 243
20100E3 - 243

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: 30608.977 Da / Num. of mol.: 5 / Mutation: K101 deletion
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 7% PEG4000, 0.4M NH4SCN, 0.1M Citric acid(pH7.3)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 27942 / Num. obs: 27942 / % possible obs: 99.2 % / Redundancy: 11 % / Net I/σ(I): 26.2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAR, 2B98

2oar

2b98


Resolution: 3.5→42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.935 / SU B: 50.294 / SU ML: 0.709 / Cross valid method: THROUGHOUT / ESU R Free: 0.596 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28709 1455 5.1 %RANDOM
Rwork0.25949 ---
obs0.26085 27306 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 170.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.5 Å2-0 Å20 Å2
2--12.95 Å20 Å2
3----8.45 Å2
Refinement stepCycle: LAST / Resolution: 3.5→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 0 0 9218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199406
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9812743
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.56951209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13725.109321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.458151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0611516
X-RAY DIFFRACTIONr_chiral_restr0.0880.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216784
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_it8.54517.4294858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.80526.1426060
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.17118.0164548
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined18.47739805
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)
11A5940.1
12B5940.1
21A5780.12
22C5780.12
31A5920.12
32D5920.12
41A5880.12
42E5880.12
51B5880.11
52C5880.11
61B6000.1
62D6000.1
71B6000.1
72E6000.1
81C5940.12
82D5940.12
91C5980.12
92E5980.12
101D6080.11
102E6080.11
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 107 -
Rwork0.401 1981 -
obs--100 %

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