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- PDB-6qlk: Crystal structure of F181H UbiX in complex with prFMN -

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Basic information

Entry
Database: PDB / ID: 6qlk
TitleCrystal structure of F181H UbiX in complex with prFMN
ComponentsFlavin prenyltransferase UbiX
KeywordsTRANSFERASE / UbiX Prenyltransferase Flavin binding
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-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-4LU / PHOSPHATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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 / _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)25,4314
Polymers24,7871
Non-polymers6433
Water2,288127
1
A: Flavin prenyltransferase UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)305,16948
Polymers297,44712
Non-polymers7,72136
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 area58200 Å2
ΔGint-487 kcal/mol
Surface area66050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.751, 141.751, 141.751
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-505-

HOH

21A-506-

HOH

31A-507-

HOH

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Components

#1: Protein Flavin prenyltransferase UbiX


Mass: 24787.291 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-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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: LMB screen (Molecular Dimensions) condition F2 16 % w/v PEG 4000, 20 % v/v glycerol, 0.1 M sodium citrate pH 5.8, 0.1 M ammonium sulphate

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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: 1.78→35.44 Å / Num. obs: 22624 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.08218 / Net I/σ(I): 12.99
Reflection shellResolution: 1.78→1.844 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: 1.78→35.44 Å / SU ML: 0.2216 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5096
RfactorNum. reflection% reflection
Rfree0.2116 1181 5.26 %
Rwork0.1875 --
obs0.1888 22440 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.64 Å2
Refinement stepCycle: LAST / Resolution: 1.78→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 42 127 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721594
X-RAY DIFFRACTIONf_angle_d1.01472193
X-RAY DIFFRACTIONf_chiral_restr0.1193257
X-RAY DIFFRACTIONf_plane_restr0.0058282
X-RAY DIFFRACTIONf_dihedral_angle_d3.03151298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.38471320.3282602X-RAY DIFFRACTION97.96
1.86-1.960.30651760.29012618X-RAY DIFFRACTION98.52
1.96-2.080.28441190.25222658X-RAY DIFFRACTION98.9
2.08-2.240.24771350.21282668X-RAY DIFFRACTION100
2.24-2.470.22271390.19462663X-RAY DIFFRACTION99.36
2.47-2.830.23211640.18752644X-RAY DIFFRACTION99.75
2.83-3.560.18131420.16212722X-RAY DIFFRACTION99.76
3.56-35.440.16261740.14332684X-RAY DIFFRACTION97.88

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