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

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Basic information

Entry
Database: PDB / ID: 3udc
TitleCrystal structure of a membrane protein
ComponentsSmall-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
KeywordsMEMBRANE PROTEIN / channel / Mechanosensitive
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / membrane / identical protein binding / plasma membrane
Similarity search - Function
Mechanosensitive ion channel YbiO / Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 ...Mechanosensitive ion channel YbiO / Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / 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 / 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 / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.355 Å
AuthorsLi, W. / Ge, J. / Yang, M.
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
DepositionOct 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
B: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
C: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
D: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
E: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
F: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
G: Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel


Theoretical massNumber of molelcules
Total (without water)227,2357
Polymers227,2357
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42820 Å2
ΔGint-330 kcal/mol
Surface area87820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.046, 139.468, 224.113
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 13 - 279 / Label seq-ID: 13 - 279

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 13:279 )AA
2chain B and (resseq 13:279 )BB
3chain C and (resseq 13:279 )CC
4chain D and (resseq 13:279 )DD
5chain E and (resseq 13:279 )EE
6chain F and (resseq 13:279 )FF
7chain G and (resseq 13:279 )GG

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Components

#1: Protein
Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel


Mass: 32462.180 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: chimera of Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria), (gene. exp.) Escherichia coli (E. coli)
Strain: MB4, K-12 / Gene: MscS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R6L9, UniProt: P0C0S1

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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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM NaCl, 30% PEG 400(pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2011
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.355→42.083 Å / Num. obs: 43482 / % possible obs: 99.2 % / Biso Wilson estimate: 111.87 Å2
Reflection shellResolution: 3.35→3.47 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
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: 3.355→42.083 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7231 / SU ML: 1.06 / σ(F): 1.34 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1878 4.33 %thin shell
Rwork0.2477 ---
obs0.249 43408 98.9 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.592 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 279.64 Å2 / Biso mean: 141.4308 Å2 / Biso min: 51.38 Å2
Baniso -1Baniso -2Baniso -3
1--26.139 Å20 Å2-0 Å2
2--24.269 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 3.355→42.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14903 0 0 0 14903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115155
X-RAY DIFFRACTIONf_angle_d1.320405
X-RAY DIFFRACTIONf_chiral_restr0.0842380
X-RAY DIFFRACTIONf_plane_restr0.0052534
X-RAY DIFFRACTIONf_dihedral_angle_d22.6959429
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2129X-RAY DIFFRACTIONPOSITIONAL0.054
12B2129X-RAY DIFFRACTIONPOSITIONAL0.054
13C2129X-RAY DIFFRACTIONPOSITIONAL0.052
14D2129X-RAY DIFFRACTIONPOSITIONAL0.056
15E2129X-RAY DIFFRACTIONPOSITIONAL0.065
16F2129X-RAY DIFFRACTIONPOSITIONAL0.054
17G2129X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Num. reflection all
3.3549-3.44560.3588322896
3.4456-3.54690.343323100
3.5469-3.66140.30943283100
3.6614-3.79210.33056270.293627121003339
3.7921-3.94390.28233347100
3.9439-4.12320.24153336100
4.1232-4.34040.21263342100
4.3404-4.6120.25445750.189327661003341
4.612-4.96760.2081332599
4.9676-5.46650.24883379100
5.4665-6.25530.35894270.276529761003403
6.2553-7.87260.23113415100
7.8726-42.08620.22242490.24173098933347
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)
10.2726-0.17880.10220.3524-0.33990.12590.0001-0.1457-0.4115-0.0646-0.08520.2329-0.0661-0.00010.00010.958-0.10450.03040.878-0.05631.0695-37.44869.7641-53.7
20.1651-0.2037-0.005-0.37240.03430.18080.1275-0.3434-0.4613-0.00860.0610.0679-0.08020.24190.00090.9779-0.02870.01660.7866-0.03280.8602-22.785811.2174-43.6137
30.0462-0.3788-0.0720.25350.26810.54540.2089-0.00510.21710.0524-0.0724-0.0931-0.4751-0.1142-0.00010.84090.02250.04250.7681-0.09220.7861-19.525643.1553-39.8462
40.92770.3025-0.09730.30440.1327-0.0254-0.20410.4223-0.4155-0.0783-0.12720.1830.1335-0.333400.7770.0685-0.05821.0555-0.0370.9835-47.740922.9578-60.1103
50.28220.00180.08210.07830.10970.1057-0.09610.3885-0.2297-0.0762-0.04870.0996-0.2237-0.7796-0.00080.81350.0912-0.00650.9615-0.08580.7452-45.836440.5442-57.9931
60.5661-0.4756-0.0327-0.31090.19520.29530.10010.03440.0325-0.0338-0.0307-0.0295-0.4433-0.314-0.00020.94840.04510.11660.70940.00740.9586-33.384149.5926-49.0292
70.00040.263-0.0849-0.07070.22360.55650.109-0.5511-0.22370.0294-0.0188-0.117-0.35320.4507-0.00120.77720.11370.04580.85650.00050.8701-14.840125.9946-37.4365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA13 - 279
2X-RAY DIFFRACTION2chain BB13 - 279
3X-RAY DIFFRACTION3chain CC13 - 279
4X-RAY DIFFRACTION4chain DD13 - 279
5X-RAY DIFFRACTION5chain EE13 - 279
6X-RAY DIFFRACTION6chain FF13 - 279
7X-RAY DIFFRACTION7chain GG13 - 279

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