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- PDB-6qlh: Crystal structure of UbiX in complex with reduced FMN and isopent... -

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Basic information

Entry
Database: PDB / ID: 6qlh
TitleCrystal structure of UbiX in complex with reduced FMN and isopentyl monophosphate
ComponentsFlavin prenyltransferase UbiX
KeywordsTRANSFERASE / UbiX Prenyltransferase Flavin binding
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / lyase activity / nucleotide binding
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-FNR / Isopentenyl phosphate / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMarshall, S.A. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P000622/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry.
Authors: Marshall, S.A. / Payne, K.A.P. / Fisher, K. / White, M.D. / Ni Cheallaigh, A. / Balaikaite, A. / Rigby, S.E.J. / Leys, D.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.identifier_ORCID
Revision 1.2Jan 24, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin prenyltransferase UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4444
Polymers24,7961
Non-polymers6473
Water3,549197
1
A: Flavin prenyltransferase UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)305,32548
Polymers297,55612
Non-polymers7,77036
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation17_545z,x-1/2,y+1/21
crystal symmetry operation18_544z,-x-1/2,-y-1/21
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation45_545y+1/2,z-1/2,x1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
crystal symmetry operation48_445-y-1/2,-z-1/2,x1
Buried area70440 Å2
ΔGint-450 kcal/mol
Surface area68670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.124, 142.124, 142.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Space group name HallF223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x,y+1/2,z+1/2
#14: z,x+1/2,y+1/2
#15: y,z+1/2,x+1/2
#16: -y,-z+1/2,x+1/2
#17: z,-x+1/2,-y+1/2
#18: -y,z+1/2,-x+1/2
#19: -z,-x+1/2,y+1/2
#20: -z,x+1/2,-y+1/2
#21: y,-z+1/2,-x+1/2
#22: x,-y+1/2,-z+1/2
#23: -x,y+1/2,-z+1/2
#24: -x,-y+1/2,z+1/2
#25: x+1/2,y,z+1/2
#26: z+1/2,x,y+1/2
#27: y+1/2,z,x+1/2
#28: -y+1/2,-z,x+1/2
#29: z+1/2,-x,-y+1/2
#30: -y+1/2,z,-x+1/2
#31: -z+1/2,-x,y+1/2
#32: -z+1/2,x,-y+1/2
#33: y+1/2,-z,-x+1/2
#34: x+1/2,-y,-z+1/2
#35: -x+1/2,y,-z+1/2
#36: -x+1/2,-y,z+1/2
#37: x+1/2,y+1/2,z
#38: z+1/2,x+1/2,y
#39: y+1/2,z+1/2,x
#40: -y+1/2,-z+1/2,x
#41: z+1/2,-x+1/2,-y
#42: -y+1/2,z+1/2,-x
#43: -z+1/2,-x+1/2,y
#44: -z+1/2,x+1/2,-y
#45: y+1/2,-z+1/2,-x
#46: x+1/2,-y+1/2,-z
#47: -x+1/2,y+1/2,-z
#48: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

21A-549-

HOH

31A-553-

HOH

41A-557-

HOH

51A-559-

HOH

61A-597-

HOH

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Components

#1: Protein Flavin prenyltransferase UbiX


Mass: 24796.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ubiX, C0044_29760, C8257_05245, CAZ10_26235, CGU42_07325, DT376_15100, DZ940_19110, DZ962_23875, NCTC13719_00955, PAERUG_E15_London_28_01_14_05236, PAMH19_1010, RW109_RW109_01660
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZCW8, flavin prenyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IP8 / Isopentenyl phosphate / 3-methylbut-3-en-1-yl dihydrogen phosphate


Mass: 166.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H11O4P
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: SG1 screen (Molecular Dimensions) F4 1 M sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→24.02 Å / Num. obs: 33160 / % possible obs: 99.19 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1061 / Net I/σ(I): 10.09
Reflection shellResolution: 1.57→1.626 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZAF

4zaf


Resolution: 1.57→24.02 Å / SU ML: 0.181 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.298
RfactorNum. reflection% reflection
Rfree0.199 1731 5.26 %
Rwork0.1773 --
obs0.1785 32908 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.35 Å2
Refinement stepCycle: LAST / Resolution: 1.57→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 42 197 1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451631
X-RAY DIFFRACTIONf_angle_d0.75682230
X-RAY DIFFRACTIONf_chiral_restr0.0471256
X-RAY DIFFRACTIONf_plane_restr0.0043291
X-RAY DIFFRACTIONf_dihedral_angle_d3.10681356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.620.35241460.32232548X-RAY DIFFRACTION98.07
1.62-1.670.39841310.29682531X-RAY DIFFRACTION98.3
1.67-1.730.32211390.28332575X-RAY DIFFRACTION98.4
1.73-1.80.29131360.25042568X-RAY DIFFRACTION98.98
1.8-1.880.22681440.2192581X-RAY DIFFRACTION99.2
1.88-1.980.20941550.20092595X-RAY DIFFRACTION99.46
1.98-2.10.23561820.18522529X-RAY DIFFRACTION99.16
2.1-2.260.18481340.16442639X-RAY DIFFRACTION100
2.26-2.490.18481210.15962616X-RAY DIFFRACTION99.74
2.49-2.850.16571490.16232638X-RAY DIFFRACTION99.86
2.85-3.590.18981310.14642665X-RAY DIFFRACTION99.96
3.59-24.030.13291630.13472692X-RAY DIFFRACTION99.9

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