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- PDB-4zax: Structure of UbiX in complex with oxidised prenylated FMN (radical) -

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Basic information

Entry
Database: PDB / ID: 4zax
TitleStructure of UbiX in complex with oxidised prenylated FMN (radical)
ComponentsUbiX
KeywordsTRANSFERASE / prenyl transferase / flavin binding / UbiX
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / prenyltransferase activity / carboxy-lyase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4LU / PHOSPHATE ION / THIOCYANATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsWhite, M.D. / Leys, D.
CitationJournal: Nature / Year: 2015
Title: UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis.
Authors: White, M.D. / Payne, K.A. / Fisher, K. / Marshall, S.A. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1796
Polymers22,3851
Non-polymers7955
Water2,288127
1
A: UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)278,15372
Polymers268,61712
Non-polymers9,53660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area72670 Å2
ΔGint-453 kcal/mol
Surface area67100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.790, 141.790, 141.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-491-

HOH

21A-513-

HOH

31A-521-

HOH

41A-527-

HOH

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Components

#1: Protein UbiX


Mass: 22384.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4019 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HX08, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O9P
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 3350, 150mM sodium thiocyanate and 100mM Tris pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.61→42.75 Å / Num. obs: 29027 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 20.1
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→42.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.449 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17095 1541 5 %RANDOM
Rwork0.1436 ---
obs0.14493 29027 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.876 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.61→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 50 127 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191714
X-RAY DIFFRACTIONr_bond_other_d0.0040.021653
X-RAY DIFFRACTIONr_angle_refined_deg2.43122357
X-RAY DIFFRACTIONr_angle_other_deg1.7343.0053811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01124.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7111511
X-RAY DIFFRACTIONr_chiral_restr0.2760.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211962
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3192.025866
X-RAY DIFFRACTIONr_mcbond_other2.3112.022863
X-RAY DIFFRACTIONr_mcangle_it3.2443.0221085
X-RAY DIFFRACTIONr_mcangle_other3.2433.0231086
X-RAY DIFFRACTIONr_scbond_it3.5492.437848
X-RAY DIFFRACTIONr_scbond_other3.5382.436846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3063.511261
X-RAY DIFFRACTIONr_long_range_B_refined6.49817.7071995
X-RAY DIFFRACTIONr_long_range_B_other6.49617.7121996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 110 -
Rwork0.243 2159 -
obs--99.91 %

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