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- PDB-6h6p: UbiJ-SCP2 Ubiquinone synthesis protein -

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Basic information

Entry
Database: PDB / ID: 6h6p
TitleUbiJ-SCP2 Ubiquinone synthesis protein
ComponentsUbiquinone biosynthesis protein UbiJCoenzyme Q10
KeywordsLIPID BINDING PROTEIN / SCP2 Lipid binding protein Ubiquinone synthesis protein
Function / homology
Function and homology information


ubiquinone biosynthetic process from chorismate / ubiquinone biosynthesis complex / ubiquinone biosynthetic process / identical protein binding / cytoplasm
Similarity search - Function
Ubiquinone biosynthesis accessory factor UbiJ / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily
Similarity search - Domain/homology
Ubiquinone biosynthesis accessory factor UbiJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFyfe, C.D. / Legrand, P. / Pecqueur, L. / Ciccone, L. / Lombard, M. / Fontecave, M.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: Cell Chem Biol / Year: 2019
Title: A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone.
Authors: Hajj Chehade, M. / Pelosi, L. / Fyfe, C.D. / Loiseau, L. / Rascalou, B. / Brugiere, S. / Kazemzadeh, K. / Vo, C.D. / Ciccone, L. / Aussel, L. / Coute, Y. / Fontecave, M. / Barras, F. / Lombard, M. / Pierrel, F.
History
DepositionJul 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquinone biosynthesis protein UbiJ
B: Ubiquinone biosynthesis protein UbiJ
C: Ubiquinone biosynthesis protein UbiJ
D: Ubiquinone biosynthesis protein UbiJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,72122
Polymers58,6034
Non-polymers1,11818
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-153 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.690, 94.550, 115.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ubiquinone biosynthesis protein UbiJ / Coenzyme Q10


Mass: 14650.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ubiJ, yigP, b3834, JW3811 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADP7
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 225 mM Calcium Chloride, 100 mM MMT buffer pH 9, 11% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→47.28 Å / Num. obs: 18749 / % possible obs: 99.92 % / Redundancy: 7.4 % / Biso Wilson estimate: 72.21 Å2 / Net I/σ(I): 9.13
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H6N

6h6n


Resolution: 2.5→47.28 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.897 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.589 / SU Rfree Blow DPI: 0.319 / SU Rfree Cruickshank DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.289 938 5 %RANDOM
Rwork0.233 ---
obs0.236 18749 100 %-
Displacement parametersBiso mean: 79.12 Å2
Baniso -1Baniso -2Baniso -3
1--4.8724 Å20 Å20 Å2
2---3.3669 Å20 Å2
3---8.2393 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.5→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 48 89 3716
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013710HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.275062HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1315SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it3710HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion19.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4092SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.258 149 5 %
Rwork0.224 2831 -
all0.226 2980 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8796-0.48610.73014.13252.30046.4022-0.0781-0.0870.183-0.2995-0.1373-0.0616-0.5656-0.38540.2153-0.63190.042-0.0191-0.8711-0.0731-0.6931-14.904114.1337-2.1779
22.04040.5719-0.62842.5751.48523.56460.07480.0176-0.02520.2087-0.00960.08930.5228-0.0716-0.0652-0.67390.0124-0.0145-0.90460.0106-0.7355-6.2716-14.4072-1.8235
33.3259-0.0998-0.59872.50260.64694.7842-0.00370.0154-0.1008-0.0279-0.05220.2291-0.2579-0.42290.0559-0.79590.0252-0.0301-0.7679-0.0326-0.7507-23.89038.021724.014
46.8148-1.1862-0.24723.04690.96973.842-0.1662-0.2173-0.1180.23960.0583-0.43240.33010.42670.1079-0.78310.02550.0238-0.8175-0.0365-0.7698-0.415-9.587724.0835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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