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- PDB-4zal: Structure of UbiX E49Q mutant in complex with reduced FMN and dim... -

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Basic information

Entry
Database: PDB / ID: 4zal
TitleStructure of UbiX E49Q mutant in complex with reduced FMN and dimethylallyl monophosphate
ComponentsUbiX
KeywordsLYASE / prenyl transferase / UbiX / FMN binding
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
Dimethylallyl monophosphate / Chem-FNR / THIOCYANATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 13, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
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: UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1245
Polymers22,3841
Non-polymers7414
Water2,504139
1
A: UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)277,49360
Polymers268,60512
Non-polymers8,88848
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 area69730 Å2
ΔGint-322 kcal/mol
Surface area70020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.070, 142.070, 142.070
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-496-

HOH

21A-519-

HOH

31A-523-

HOH

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Components

#1: Protein UbiX


Mass: 22383.756 Da / Num. of mol.: 1 / Mutation: E49Q
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-4LR / Dimethylallyl monophosphate


Mass: 166.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O4P
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
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: I03 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→42.84 Å / Num. obs: 28593 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rpim(I) all: 0.024 / Net I/σ(I): 16.9
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.8 / Rpim(I) all: 0.292 / % 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: 1.62→42.84 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.553 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16345 1525 5.1 %RANDOM
Rwork0.13967 ---
obs0.14091 28593 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.468 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.62→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 47 139 1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021754
X-RAY DIFFRACTIONr_bond_other_d0.0030.021678
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.9932406
X-RAY DIFFRACTIONr_angle_other_deg1.0393.0053857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11324.02872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1381514
X-RAY DIFFRACTIONr_chiral_restr0.3020.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02395
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_it2.5782.346896
X-RAY DIFFRACTIONr_mcbond_other2.5762.349897
X-RAY DIFFRACTIONr_mcangle_it3.4993.4961136
X-RAY DIFFRACTIONr_mcangle_other3.4973.51137
X-RAY DIFFRACTIONr_scbond_it4.2242.799858
X-RAY DIFFRACTIONr_scbond_other4.1862.792855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3034.0191267
X-RAY DIFFRACTIONr_long_range_B_refined7.28920.6922083
X-RAY DIFFRACTIONr_long_range_B_other7.2220.2472021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 108 -
Rwork0.235 2065 -
obs--99.95 %

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