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- PDB-6y86: Active YidC insertase crystal structure with the first transmembr... -

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Basic information

Entry
Database: PDB / ID: 6y86
TitleActive YidC insertase crystal structure with the first transmembrane domain resolved
ComponentsMembrane protein insertase YidC
KeywordsMEMBRANE PROTEIN / Insertase and chaperone
Function / homology
Function and homology information


membrane insertase activity / protein insertion into membrane / protein transport / plasma membrane
Similarity search - Function
Membrane insertase YidC / : / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18
Similarity search - Domain/homology
Membrane protein insertase YidC
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLi, X.D. / Nass, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2022
Title: The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations.
Authors: Nass, K.J. / Ilie, I.M. / Saller, M.J. / Driessen, A.J.M. / Caflisch, A. / Kammerer, R.A. / Li, X.
History
DepositionMar 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)49,2011
Polymers49,2011
Non-polymers00
Water00
1
A: Membrane protein insertase YidC

A: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)98,4022
Polymers98,4022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1630 Å2
ΔGint-25 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.590, 122.590, 97.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Membrane protein insertase YidC / Foldase YidC / Membrane integrase YidC / Membrane protein YidC


Mass: 49201.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: yidC, TM_1461 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H2

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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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Bis-Tris, pH5.5, 0.2M di-ammonium hydrogen citrate with 24% PEG 3350.
PH range: 4.6-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Oct 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.55 Å / Num. obs: 10680 / % possible obs: 100 % / Redundancy: 30.1 % / CC1/2: 1 / Net I/σ(I): 13.7
Reflection shellResolution: 3.4→20 Å / Num. unique obs: 10052 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIXdev_2645refinement
PDB_EXTRACT3.25data extraction
XDSv1.0data reduction
XDSv1.0data scaling
PHASERv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: experiment

Resolution: 3.4→19.994 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.43
RfactorNum. reflection% reflection
Rfree0.3012 526 4.97 %
Rwork0.2616 --
obs0.2635 10577 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 405.26 Å2 / Biso mean: 156.3716 Å2 / Biso min: 64.29 Å2
Refinement stepCycle: final / Resolution: 3.4→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 0 0 3487
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043583
X-RAY DIFFRACTIONf_angle_d0.7934871
X-RAY DIFFRACTIONf_chiral_restr0.045553
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d18.4742087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.4-3.74020.3491290.31612458
3.7402-4.27680.31891290.27282458
4.2768-5.37090.27911320.23822510
5.3709-100.30021360.26332625
Refinement TLS params.Method: refined / Origin x: -18.1047 Å / Origin y: -10.5926 Å / Origin z: -24.1688 Å
111213212223313233
T0.8137 Å2-0.0584 Å2-0.0262 Å2-0.623 Å2-0.0123 Å2--0.7774 Å2
L4.3036 °2-0.8762 °2-0.313 °2-2.4323 °20.3281 °2--3.9899 °2
S0.0457 Å °0.4724 Å °-0.1095 Å °-0.3421 Å °-0.0848 Å °-0.4408 Å °-0.0108 Å °0.0558 Å °0.0321 Å °
Refinement TLS groupSelection details: all

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