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- PDB-5y83: Crystal structure of YidC from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 5y83
TitleCrystal structure of YidC from Thermotoga maritima
ComponentsMembrane protein insertase YidC
KeywordsTRANSPORT PROTEIN / yidc / alb3 / oxa1 / sec
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: 3.842 Å
AuthorsHuang, Y. / Xin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2013CB910603 China
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
A: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)52,2621
Polymers52,2621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17050 Å2
Unit cell
Length a, b, c (Å)75.745, 103.600, 129.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 52261.875 Da / Num. of mol.: 1 / Mutation: T24V, K25V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: yidC, TM_1461 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 4.87 Å3/Da / Density % sol: 81.04 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 20% PEG1500(w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 10459 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.128 / Χ2: 1.048 / Net I/σ(I): 4.4 / Num. measured all: 85442
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.8-3.948.310190.5390.940.926100
3.94-4.098.410160.720.6710.94100
4.09-4.288.410300.9350.3250.9531000.9020.961
4.28-4.58.310310.9690.181.0481000.4970.529
4.5-4.798.310410.990.1091.1241000.30.32
4.79-5.168.310320.990.1051.1041000.2910.31
5.16-5.678.210450.9820.11.0631000.2720.291
5.67-6.497.910560.9840.0781.0781000.2090.223
6.49-8.188.110710.9970.0361.1531000.10.106
8.18-507.511180.9970.0241.08997.10.0610.066

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.842→42.758 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3124 729 5.16 %
Rwork0.2635 --
obs0.266 10459 75.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.72 Å2 / Biso mean: 69.7552 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 3.842→42.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 0 0 2679
Num. residues----342

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