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- PDB-4zan: Structure of UbiX Y169F in complex with oxidised FMN and dimethyl... -

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Basic information

Entry
Database: PDB / ID: 4zan
TitleStructure of UbiX Y169F in complex with oxidised FMN and dimethylallyl monophosphate
ComponentsUbiX
KeywordsLYASE / prenyl transferase / flavin binding / UbiX
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity / prenyltransferase 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 / FLAVIN MONONUCLEOTIDE / : / THIOCYANATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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)23,1466
Polymers22,3691
Non-polymers7785
Water2,090116
1
A: UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)277,75772
Polymers268,42512
Non-polymers9,33360
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 area69850 Å2
ΔGint-335 kcal/mol
Surface area69240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.730, 141.730, 141.730
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-59-

GLN

21A-475-

HOH

31A-497-

HOH

41A-499-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UbiX


Mass: 22368.740 Da / Num. of mol.: 1 / Mutation: Y169F
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

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-4LR / Dimethylallyl monophosphate


Mass: 166.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O4P
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 53.61 %
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: 1.76→70.86 Å / Num. obs: 22355 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rpim(I) all: 0.026 / Net I/σ(I): 19.3
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.4 / Rpim(I) all: 0.36 / % 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: 1.76→70.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.087 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18197 1074 4.6 %RANDOM
Rwork0.14243 ---
obs0.14423 22355 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.668 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.76→70.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 48 116 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021678
X-RAY DIFFRACTIONr_bond_other_d0.0030.021611
X-RAY DIFFRACTIONr_angle_refined_deg2.4071.9962296
X-RAY DIFFRACTIONr_angle_other_deg1.1813.0053704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4825218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.00424.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43915260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9241510
X-RAY DIFFRACTIONr_chiral_restr0.3030.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211925
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02364
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_it2.5312.392859
X-RAY DIFFRACTIONr_mcbond_other2.5312.392860
X-RAY DIFFRACTIONr_mcangle_it3.4473.5741080
X-RAY DIFFRACTIONr_mcangle_other3.4473.5751081
X-RAY DIFFRACTIONr_scbond_it3.7952.808819
X-RAY DIFFRACTIONr_scbond_other3.7992.807816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6444.0461215
X-RAY DIFFRACTIONr_long_range_B_refined7.91320.5761952
X-RAY DIFFRACTIONr_long_range_B_other7.91220.5811953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 70 -
Rwork0.231 1639 -
obs--100 %

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