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- PDB-3t9n: Crystal structure of a membrane protein -

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Basic information

Entry
Database: PDB / ID: 3t9n
TitleCrystal structure of a membrane protein
ComponentsSmall-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / channel
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / identical protein binding / plasma membrane
Similarity search - Function
Mechanosensitive ion channel YbiO / Helix Hairpins - #1260 / SH3 type barrels. - #60 / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS ...Mechanosensitive ion channel YbiO / Helix Hairpins - #1260 / SH3 type barrels. - #60 / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / 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 / Alpha-Beta Plaits - #100 / LSM domain superfamily / SH3 type barrels. / Helix Hairpins / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.456 Å
AuthorsYang, M. / Zhang, X. / Ge, J. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and molecular mechanism of an anion-selective mechanosensitive channel of small conductance
Authors: Zhang, X. / Wang, J. / Feng, Y. / Ge, J. / Li, W. / Sun, W. / Iscla, I. / Yu, J. / Blount, P. / Li, Y. / Yang, M.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,5239
Polymers224,5027
Non-polymers1,0212
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45240 Å2
ΔGint-352 kcal/mol
Surface area91710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.029, 138.627, 214.580
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
31C
41D
51E
61F
71G

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRASPASPchain A and (resseq 13:213 or resseq 217:281 )AA13 - 21313 - 213
12GLUGLUTHRTHRchain A and (resseq 13:213 or resseq 217:281 )AA217 - 281217 - 281
21TYRTYRARGARGchain B and (resseq 13:212 or resseq 218:281 )BB13 - 21213 - 212
22GLYGLYTHRTHRchain B and (resseq 13:212 or resseq 218:281 )BB218 - 281218 - 281
31TYRTYRARGARGchain C and (resseq 13:212 or resseq 218:281 )CC13 - 21213 - 212
32GLYGLYTHRTHRchain C and (resseq 13:212 or resseq 218:281 )CC218 - 281218 - 281
41TYRTYRARGARGchain D and (resseq 13:212 or resseq 217:281 )DD13 - 21213 - 212
42GLUGLUTHRTHRchain D and (resseq 13:212 or resseq 217:281 )DD217 - 281217 - 281
51TYRTYRARGARGchain E and (resseq 13:212 or resseq 218:281 )EE13 - 21213 - 212
52GLYGLYTHRTHRchain E and (resseq 13:212 or resseq 218:281 )EE218 - 281218 - 281
61TYRTYRARGARGchain F and (resseq 13:212 or resseq 218:281 )FF13 - 21213 - 212
62GLYGLYTHRTHRchain F and (resseq 13:212 or resseq 218:281 )FF218 - 281218 - 281
71TYRTYRARGARGchain G and (resseq 13:212 or resseq 218:281 )GG13 - 21213 - 212
72GLYGLYTHRTHRchain G and (resseq 13:212 or resseq 218:281 )GG218 - 281218 - 281

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Components

#1: Protein
Small-conductance mechanosensitive channel


Mass: 32071.740 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Gene: MscS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R6L9
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10%(v/v) 2-Propanol, 0.1M sodium citrate tribasic dehydrate, 22%(w/v) polyethylene glycol 400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2010
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.445→50 Å / Num. obs: 36145 / % possible obs: 95.7 % / Observed criterion σ(I): 1.45 / Biso Wilson estimate: 110.03 Å2
Reflection shellResolution: 3.445→3.57 Å / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAU

2oau


Resolution: 3.456→38.738 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7724 / SU ML: 0.98 / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 1801 4.99 %Random
Rwork0.2526 ---
obs0.2544 36108 95.37 %-
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.044 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 487.75 Å2 / Biso mean: 136.5872 Å2 / Biso min: 55.04 Å2
Baniso -1Baniso -2Baniso -3
1--3.4316 Å2-0 Å20 Å2
2---9.9056 Å2-0 Å2
3---13.3372 Å2
Refinement stepCycle: LAST / Resolution: 3.456→38.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14719 0 70 0 14789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115022
X-RAY DIFFRACTIONf_angle_d1.37720212
X-RAY DIFFRACTIONf_chiral_restr0.0872396
X-RAY DIFFRACTIONf_plane_restr0.0052470
X-RAY DIFFRACTIONf_dihedral_angle_d22.1979355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2098X-RAY DIFFRACTIONPOSITIONAL0.064
12B2098X-RAY DIFFRACTIONPOSITIONAL0.064
13C2098X-RAY DIFFRACTIONPOSITIONAL0.059
14D2107X-RAY DIFFRACTIONPOSITIONAL0.07
15E2098X-RAY DIFFRACTIONPOSITIONAL0.071
16F2098X-RAY DIFFRACTIONPOSITIONAL0.062
17G2098X-RAY DIFFRACTIONPOSITIONAL0.067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4558-3.54920.391230.30342351247487
3.5492-3.65360.31310.29022579271094
3.6536-3.77140.28951290.28072546267594
3.7714-3.90610.34051310.27752612274395
3.9061-4.06230.32581350.27442586272195
4.0623-4.2470.27191120.25112651276396
4.247-4.47060.28031360.21582611274795
4.4706-4.75020.25291490.20652647279696
4.7502-5.11620.3011400.22062700284097
5.1162-5.62970.32721380.25092736287499
5.6297-6.44110.32441400.27282749288998
6.4411-8.10290.28741700.22922740291098
8.1029-38.74090.25721670.272799296696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9432-0.5892-0.78840.95630.91861.8152-0.12350.1121-0.3265-0.06510.132-0.27430.52240.32720.061.1557-0.09030.16130.9508-0.06531.0404-11.3464-55.386151.0395
2-0.1591-0.31480.38770.48830.35291.3008-0.09170.3363-0.2705-0.3914-0.14580.19630.058-0.58410.33571.0928-0.14910.04711.1151-0.09560.9494-25.4906-53.331241.5438
31.73850.0211-1.5580.86380.00452.26680.5674-0.02260.6496-0.437-0.0330.3882-1.0277-0.0167-0.59531.0848-0.00940.06531.00430.09921.0254-28.2416-22.431838.5169
41.4769-0.9761-1.3492.15231.50412.233-0.2747-0.3977-0.28010.08320.2325-0.47040.36550.8675-0.07240.75670.03780.04810.9294-0.08311.0979-1.1993-42.88457.5781
52.1655-0.3368-1.20321.35180.43541.67380.1077-0.5460.1703-0.08820.0819-0.545-0.35470.8913-0.34540.9874-0.12810.08541.1336-0.08781.1202-2.7223-25.739956.0129
62.34710.132-1.15231.17660.11211.42070.28510.06250.4875-0.48630.0753-0.066-0.7340.3036-0.50741.0588-0.10120.12020.96620.00380.8434-14.665-16.535847.5044
70.95540.7099-1.62491.7567-1.12883.75820.07080.6132-0.2125-0.56680.06270.4766-0.425-0.5889-0.13980.91650.037-0.04571.10460.00620.9502-32.9711-38.843635.8734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 13:281A13 - 281
2X-RAY DIFFRACTION2CHAIN B AND RESID 13:281B13 - 281
3X-RAY DIFFRACTION3CHAIN C AND RESID 13:281C13 - 281
4X-RAY DIFFRACTION4CHAIN D AND RESID 13:281D13 - 281
5X-RAY DIFFRACTION5CHAIN E AND RESID 13:281E13 - 281
6X-RAY DIFFRACTION6CHAIN F AND RESID 13:281F13 - 281
7X-RAY DIFFRACTION7CHAIN G AND RESID 13:281G13 - 281

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