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- PDB-6qli: Crystal structure of F181Q UbiX in complex with FMN and dimethyla... -

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Basic information

Entry
Database: PDB / ID: 6qli
TitleCrystal structure of F181Q UbiX in complex with FMN and dimethylallyl 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
Dimethylallyl monophosphate / Chem-FNR / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)25,4254
Polymers24,7771
Non-polymers6473
Water2,882160
1
A: Flavin prenyltransferase UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)305,09748
Polymers297,32712
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 area68410 Å2
ΔGint-442 kcal/mol
Surface area67560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.499, 142.499, 142.499
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-526-

HOH

21A-529-

HOH

31A-534-

HOH

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Components

#1: Protein Flavin prenyltransferase UbiX


Mass: 24777.273 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-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: isolated from a natural source / Formula: C17H23N4O9P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: LMB screen (Molecular Dimensions) D7 15 % w/v PEG 3350, 0.1 M MES pH 6.2

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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: 1.99→42.97 Å / Num. obs: 16551 / % possible obs: 98.97 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0936 / Net I/σ(I): 11.64
Reflection shellResolution: 1.99→2.06 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: 1.99→42.97 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6731
RfactorNum. reflection% reflection
Rfree0.213 825 5.03 %
Rwork0.1817 --
obs0.1832 16386 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.61 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 42 160 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441614
X-RAY DIFFRACTIONf_angle_d0.62832209
X-RAY DIFFRACTIONf_chiral_restr0.0417255
X-RAY DIFFRACTIONf_plane_restr0.0041289
X-RAY DIFFRACTIONf_dihedral_angle_d5.58851335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.120.35421700.31152492X-RAY DIFFRACTION97.54
2.12-2.280.26651440.25022561X-RAY DIFFRACTION98.51
2.28-2.510.29651110.21452581X-RAY DIFFRACTION98.83
2.51-2.870.24881300.19892614X-RAY DIFFRACTION99.49
2.87-3.620.17741450.1642608X-RAY DIFFRACTION99.78
3.62-42.980.14841250.13542705X-RAY DIFFRACTION99.72

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