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- PDB-3wvf: Crystal structure of YidC from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3wvf
TitleCrystal structure of YidC from Escherichia coli
ComponentsMembrane protein insertase YidC
KeywordsCHAPERONE / alpha helical
Function / homology
Function and homology information


membrane insertase activity / protein transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Membrane insertase YidC, periplasmic domain / Beta-galactosidase; Chain A, domain 5 - #90 / 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 / Beta-galactosidase; Chain A, domain 5 ...Membrane insertase YidC, periplasmic domain / Beta-galactosidase; Chain A, domain 5 - #90 / 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 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKumazaki, K. / Tsukazaki, T. / Kishimoto, T. / Ishitani, R. / Nureki, O.
CitationJournal: Sci Rep / Year: 2014
Title: Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase
Authors: Kumazaki, K. / Kishimoto, T. / Furukawa, A. / Mori, H. / Tanaka, Y. / Dohmae, N. / Ishitani, R. / Tsukazaki, T. / Nureki, O.
History
DepositionMay 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane protein insertase YidC
B: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)123,7452
Polymers123,7452
Non-polymers00
Water00
1
A: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)61,8731
Polymers61,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)61,8731
Polymers61,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.729, 76.011, 91.318
Angle α, β, γ (deg.)78.08, 82.45, 77.55
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 / Fragment: UNP residues 1-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / Gene: yidC / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R4M9

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.9
Details: 25% poly(ethyleneglycol) 600, 100mM MES-NaOH, 50mM potassium thiocyanate, 12mM triglycine, pH 5.9, LIPID CUBIC PHASE (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 8, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 16696 / Biso Wilson estimate: 36.13 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Phaser-MR)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser-MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BS6

3bs6


Resolution: 3.2→33.881 Å / FOM work R set: 0.7856 / SU ML: 0.54 / σ(F): 2.14 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 1652 10.03 %Randam
Rwork0.2214 ---
obs0.2269 16470 91.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 34.01 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6943 0 0 0 6943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037125
X-RAY DIFFRACTIONf_angle_d0.779718
X-RAY DIFFRACTIONf_chiral_restr0.0281083
X-RAY DIFFRACTIONf_plane_restr0.0051243
X-RAY DIFFRACTIONf_dihedral_angle_d13.8842528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.29410.38061370.32591219135689
3.2941-3.40040.34721360.29391198133490
3.4004-3.52180.34161400.26451239137991
3.5218-3.66260.31091370.24361232136993
3.6626-3.82910.30941420.22781280142294
3.8291-4.03070.2641350.21491243137894
4.0307-4.28280.23841450.20211315146095
4.2828-4.61270.25891000.194888798767
4.6127-5.07550.24161440.18671286143095
5.0755-5.80670.2711450.19791300144597
5.8067-7.30380.24691450.21881304144996
7.3038-33.88250.20821460.17251315146198

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