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- PDB-5y82: Crystal structure of the periplasmic domain of the Thermotoga mar... -

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Basic information

Entry
Database: PDB / ID: 5y82
TitleCrystal structure of the periplasmic domain of the Thermotoga maritima YidC
ComponentsMembrane protein insertase YidC
KeywordsTRANSPORT PROTEIN / YidC / Sec / Oxa1 / Alb3 / Transporter
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 MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.517 Å
AuthorsHuang, Y. / Xin, Y.
CitationJournal: FASEB J. / Year: 2018
Title: Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion
Authors: Xin, Y. / Zhao, Y. / Zheng, J. / Zhou, H. / Zhang, X.C. / Tian, C. / Huang, Y.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
D: Membrane protein insertase YidC
A: Membrane protein insertase YidC
B: Membrane protein insertase YidC
C: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)94,6564
Polymers94,6564
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-2 kcal/mol
Surface area37370 Å2
Unit cell
Length a, b, c (Å)79.952, 79.952, 135.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 23663.996 Da / Num. of mol.: 4 / Fragment: UNP residues 24-222 / Mutation: L57M,I105M,L153M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: yidC, TM_1461 / Plasmid: pET20b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1H2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 9 / Details: 0.05M Glycine (pH 9.0) and 55%PEG400(w/v) / PH range: 8.5-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 28926 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.045 / Rrim(I) all: 0.134 / Χ2: 0.942 / Net I/σ(I): 8.4 / Num. measured all: 293966
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.549.614430.710.4841.00599.9
2.54-2.599.914190.7790.4131.00699.9
2.59-2.6410.114490.8070.3730.97599.9
2.64-2.6910.214170.8690.3230.98199.90.987
2.69-2.7510.214780.8040.2970.97899.90.910.957
2.75-2.8210.214350.8840.2540.95199.90.7770.818
2.82-2.8910.314150.8870.2010.91799.90.6150.647
2.89-2.9610.214540.9210.1750.91499.90.5380.566
2.96-3.0510.314550.9380.1290.88199.90.3970.418
3.05-3.1510.314150.9560.10.86399.90.3060.322
3.15-3.2610.314610.9650.080.8271000.2450.258
3.26-3.3910.314420.980.0610.8541000.1870.196
3.39-3.5510.314450.9780.0510.8541000.1570.165
3.55-3.7310.314470.9810.0440.9061000.1340.141
3.73-3.9710.314520.990.0390.8911000.120.126
3.97-4.2710.214530.9880.0371.0431000.1140.12
4.27-4.710.214480.9890.0361.1261000.110.116
4.7-5.3810.214620.9880.0371.0621000.1120.118
5.38-6.769.914580.9820.0330.88899.90.10.105
6.76-301014780.980.0340.92299.50.1020.108

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000v706data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.517→29.966 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1297 5.1 %
Rwork0.2205 --
obs0.2226 25450 88.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.16 Å2 / Biso mean: 34.2801 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.517→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 0 137 6581
Biso mean---31.95 -
Num. residues----796

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