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- PDB-6al2: Crystal structure of E. coli YidC at 2.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 6al2
TitleCrystal structure of E. coli YidC at 2.8 A resolution
ComponentsMembrane protein insertase YidC
KeywordsCHAPERONE / Transmembrane / Insertase
Function / homology
Function and homology information


protein insertion into membrane from inner side / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein transport / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function
Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Membrane protein insertase YidC / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Izumioka, A. / Hamid, A.A. / Fujii, A.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119007 Japan
Japan Society for the Promotion of ScienceJP26291023 Japan
Japan Society for the Promotion of ScienceJP18H02405 Japan
Japan Society for the Promotion of ScienceJP17H05669 Japan
Japan Society for the Promotion of ScienceJP17K19528 Japan
Japan Society for the Promotion of ScienceJP16K14713 Japan
Japan Society for the Promotion of ScienceJP15H01537 Japan
Japan Society for the Promotion of ScienceJP15K06972 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: 2.8-angstrom crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop.
Authors: Tanaka, Y. / Izumioka, A. / Abdul Hamid, A. / Fujii, A. / Haruyama, T. / Furukawa, A. / Tsukazaki, T.
History
DepositionSep 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 4, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Nov 22, 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
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
B: Membrane protein insertase YidC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1023
Polymers123,7452
Non-polymers3571
Water905
1
A: Membrane protein insertase YidC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2292
Polymers61,8731
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)61,8731
Polymers61,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.910, 76.190, 91.950
Angle α, β, γ (deg.)78.030, 82.610, 78.050
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61872.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yidC, ECS88_4129 / Plasmid: pYD296 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: B7MGC7, UniProt: P25714*PLUS
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: 30% PEG 600, KSCN, Na-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→41.842 Å / Num. obs: 27283 / % possible obs: 99.8 % / Redundancy: 8.374 % / Biso Wilson estimate: 45.28 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.333 / Rrim(I) all: 0.355 / Χ2: 1.162 / Net I/σ(I): 5.64 / Num. measured all: 228470 / Scaling rejects: 497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.978.5751.3611.3444160.7531.4599.8
2.97-3.178.5080.8742.0540800.8490.93299.9
3.17-3.438.3290.5953.0339560.9050.635100
3.43-3.767.7940.464.4135660.9350.49299.9
3.76-4.28.410.2996.7832110.9660.31999.8
4.2-4.858.5930.269.4228130.9730.27798.9
4.85-5.938.4980.18710.6923770.9840.199100
5.93-8.377.8310.16511.2918510.9860.17699.9
8.37-41.8429.1540.14217.1110130.9840.1599

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å46.71 Å
Translation3 Å46.71 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.15phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVF

3wvf


Resolution: 2.8→41.842 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.66
RfactorNum. reflection% reflection
Rfree0.2749 1995 7.32 %
Rwork0.2184 --
obs0.2226 27242 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.01 Å2 / Biso mean: 59.4556 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: final / Resolution: 2.8→41.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7626 0 19 5 7650
Biso mean--84.2 37.5 -
Num. residues----964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.87010.37041430.303518251968100
2.8701-2.94770.30491390.278317491888100
2.9477-3.03440.28251450.255518361981100
3.0344-3.13230.35621420.254117891931100
3.1323-3.24420.29011440.239518171961100
3.2442-3.3740.29391410.236217871928100
3.374-3.52750.3671460.223918361982100
3.5275-3.71340.25191400.223417891929100
3.7134-3.94590.28221460.208218331979100
3.9459-4.25030.24151430.201518051948100
4.2503-4.67750.25481400.20461785192599
4.6775-5.35310.23931430.188118211964100
5.3531-6.73980.27571420.213117821924100
6.7398-41.84640.22661410.19131793193499

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