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- PDB-3wo7: Crystal structure of YidC from Bacillus halodurans (form II) -

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Basic information

Entry
Database: PDB / ID: 3wo7
TitleCrystal structure of YidC from Bacillus halodurans (form II)
ComponentsMembrane protein insertase YidC 2Biological membrane
KeywordsMEMBRANE PROTEIN / alpha helical
Function / homology
Function and homology information


membrane insertase activity / protein transport / plasma membrane
Similarity search - Function
Membrane insertase YidC/YidC1/YidC2, Firmicutes / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
COPPER (II) ION / Membrane protein insertase YidC 2
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsKumazaki, K. / Tsukazaki, T. / Ishitani, R. / Nureki, O.
CitationJournal: Nature / Year: 2014
Title: Structural basis of Sec-independent membrane protein insertion by YidC.
Authors: Kumazaki, K. / Chiba, S. / Takemoto, M. / Furukawa, A. / Nishiyama, K. / Sugano, Y. / Mori, T. / Dohmae, N. / Hirata, K. / Nakada-Nakura, Y. / Maturana, A.D. / Tanaka, Y. / Mori, H. / ...Authors: Kumazaki, K. / Chiba, S. / Takemoto, M. / Furukawa, A. / Nishiyama, K. / Sugano, Y. / Mori, T. / Dohmae, N. / Hirata, K. / Nakada-Nakura, Y. / Maturana, A.D. / Tanaka, Y. / Mori, H. / Sugita, Y. / Arisaka, F. / Ito, K. / Ishitani, R. / Tsukazaki, T. / Nureki, O.
History
DepositionDec 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Structure summary
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane protein insertase YidC 2
B: Membrane protein insertase YidC 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8386
Polymers58,5832
Non-polymers2544
Water0
1
A: Membrane protein insertase YidC 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4193
Polymers29,2921
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane protein insertase YidC 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4193
Polymers29,2921
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.033, 70.058, 82.910
Angle α, β, γ (deg.)90.000, 92.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA27 - 4300371
211chain BB27 - 272

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Components

#1: Protein Membrane protein insertase YidC 2 / Biological membrane / Foldase YidC 2 / Membrane integrase YidC 2 / Membrane protein YidC 2


Mass: 29291.682 Da / Num. of mol.: 2 / Fragment: UNP residues 27-267 / Mutation: G83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: yidC2, BH1169 / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9KDP2
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: lipidic qubic phase / pH: 6
Details: 24-26% PEG500DME, 10mM CuCl2, 200mM NH4COOH, 100mM MES-NaOH, pH 6.0, lipidic qubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.378 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 3.2→45.998 Å / Num. obs: 19141 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.55 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.2-3.40.90.4722.9612421325732360.54999.4
3.4-3.630.9570.2994.511686300630040.34799.9
3.63-3.920.9830.1787.3610935281628150.206100
3.92-4.290.9910.10811.2610121260326000.12599.9
4.29-4.790.9950.08312.745766234715290.09765.1
4.79-5.520.9960.07214.558165209420940.083100
5.52-6.740.9950.07813.476879175617540.09199.9
6.74-9.430.9980.04520.135349136513640.05399.9
9.430.9980.03526.4428387857450.04194.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
BSSdata collection
XDSdata reduction
PHENIX(Phaser-MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeM-substituted protein structure

Resolution: 3.201→45 Å / Occupancy max: 1 / Occupancy min: 0.69 / SU ML: 0.43 / σ(F): 1.35 / Phase error: 36.49 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 1898 9.92 %RANDOM
Rwork0.2599 ---
obs0.263 19127 95.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.08 Å2 / Biso mean: 96.3006 Å2 / Biso min: 53.64 Å2
Refinement stepCycle: LAST / Resolution: 3.201→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 4 0 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023678
X-RAY DIFFRACTIONf_angle_d0.7654992
X-RAY DIFFRACTIONf_chiral_restr0.024579
X-RAY DIFFRACTIONf_plane_restr0.004605
X-RAY DIFFRACTIONf_dihedral_angle_d13.2091354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1903X-RAY DIFFRACTION14.605TORSIONAL
12B1903X-RAY DIFFRACTION14.605TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.201-3.28060.37271390.33241268140799
3.2806-3.36930.37761380.31312901428100
3.3693-3.46840.35551390.280312711410100
3.4684-3.58030.33271400.274213091449100
3.5803-3.70820.36751450.28212701415100
3.7082-3.85660.27831350.274413251460100
3.8566-4.03210.28621540.251712471401100
4.0321-4.24450.3041430.256512751418100
4.2445-4.51020.29451050.2548977108299
4.5102-4.85810.2696930.230189999299
4.8581-5.34630.23891500.266312821432100
5.3463-6.11840.29021350.304912761411100
6.1184-7.70270.23011460.247212991445100
7.7027-46.0030.2551360.20581241137797

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