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- PDB-6qll: Crystal structure of F181H UbiX in complex with FMN and dimethyla... -

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Basic information

Entry
Database: PDB / ID: 6qll
TitleCrystal structure of F181H 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 / 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
Dimethylallyl monophosphate / Chem-FNR / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)25,5315
Polymers24,7871
Non-polymers7444
Water3,405189
1
A: Flavin prenyltransferase UbiX
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)306,37060
Polymers297,44712
Non-polymers8,92248
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 area70740 Å2
ΔGint-624 kcal/mol
Surface area66330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.033, 142.033, 142.033
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-629-

HOH

21A-646-

HOH

31A-647-

HOH

41A-688-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 193 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: LMB screen (Molecular Dimensions) 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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.56→23.67 Å / Num. obs: 33618 / % possible obs: 98.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.52
Reflection shellResolution: 1.56→1.62 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: 1.56→23.67 Å / SU ML: 0.1716 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9818
RfactorNum. reflection% reflection
Rfree0.1827 1735 5.22 %
Rwork0.1616 --
obs0.1627 33265 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.54 Å2
Refinement stepCycle: LAST / Resolution: 1.56→23.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 47 189 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211629
X-RAY DIFFRACTIONf_angle_d1.16852231
X-RAY DIFFRACTIONf_chiral_restr0.0779257
X-RAY DIFFRACTIONf_plane_restr0.0083291
X-RAY DIFFRACTIONf_dihedral_angle_d13.806597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.610.33521450.31342556X-RAY DIFFRACTION97.23
1.61-1.660.28611380.27992606X-RAY DIFFRACTION97.55
1.66-1.720.29191280.26112595X-RAY DIFFRACTION98.06
1.72-1.790.28481510.23812616X-RAY DIFFRACTION98.19
1.79-1.870.25251420.20372615X-RAY DIFFRACTION98.68
1.87-1.970.21341440.18532642X-RAY DIFFRACTION99.11
1.97-2.090.18951760.16792564X-RAY DIFFRACTION98.92
2.09-2.250.18761510.14722660X-RAY DIFFRACTION99.86
2.25-2.480.18421260.14522657X-RAY DIFFRACTION99.46
2.48-2.830.16981510.1522671X-RAY DIFFRACTION99.89
2.83-3.570.16121300.13032696X-RAY DIFFRACTION99.37
3.57-23.670.11941530.12562652X-RAY DIFFRACTION96.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8431164679-0.755953963663-0.3143284697011.423904891850.6787086612992.310256912280.1095958007550.1788869612570.251008281612-0.1329923697450.0227268967666-0.142100145524-0.2154362486880.147341449532-0.08493623938540.213447186797-0.01626651136970.01938173056120.1154436045270.03593074805140.1419086992543.36571738782-41.3887862873-19.1361648188
21.566685533260.121135109449-0.09399088340130.998947643620.3255031366781.63295710055-0.02053811954590.1448899706130.214400796723-0.1842483822630.0671814339561-0.117100598163-0.4348255744980.0560248686386-0.04161366187530.268946089068-0.01617648470440.01718548084380.1253309161060.05522616814340.1681428780022.38433124065-35.5088491308-19.0514072807
31.28798808481-0.102249981986-0.1796921035711.37350054065-1.078128967432.455124688170.01539032798190.1468253368530.307109599714-0.0568940148130.01319442643570.0683029935308-0.42748042757-0.1025791514660.03219024890840.2859698830060.07079351737310.009300549239310.1545093208520.06479288289140.227119434947-11.9923424613-33.0326220723-15.7363156848
41.050245427680.327577369492-0.06127592330151.64133524611-0.1167273914010.5116253093980.2784688519670.324555407027-0.0115358481547-0.0417052227516-0.1570143270280.163396644822-0.423707676164-0.335539767919-0.1093034994270.4133895058730.0549478897640.04514326443730.1342245605480.1387494667470.139303902866-4.37013999515-37.1606607032-27.4788082326
50.481542886401-0.000966683478346-0.1247475118150.4418727858040.08665272906880.8459354720320.02392890016470.07632910441980.0520392361724-0.104818567308-2.51226429617E-5-0.0163450429903-0.0822469597611-0.029160900679-0.01194815269890.153067113179-0.001078305689125.64668190904E-50.1234886404980.02797399247030.115774886742-2.40132778515-50.9614864809-16.4176273073
62.91179569256-1.15962408469-1.519635080250.7770002815110.6626824984032.20677962389-0.0450660260907-0.047696565576-0.00437126071890.0141397175590.02008713309650.003875345519680.149932470237-0.08921405258890.03572190879280.129228549541-0.0156823586134-0.01359473156270.1107724464580.00254758190680.105606759579-1.91928822806-56.2725244255-4.26784420512
70.803832347791-0.501343059654-0.1011910532340.456817947848-0.2058478426390.5765778952080.00396267574167-0.0186747285160.1990827885620.004207198675590.0124192591766-0.133162703594-0.1203123319440.0482231207661-0.01074711171960.176524969869-0.008588364527010.00844088773640.1115239229410.005858066880740.1763251835546.47281736623-38.4190957197-2.12600111442
81.40163784011-0.732247604702-1.198335964792.213582318871.87778964792.63119732613-0.00557155056161-0.008073234582330.1305568636990.0367668334434-0.0294525500158-0.0867209582673-0.1011042126150.08058643102370.04608117995590.215141181106-0.03840000586330.01085677617110.1409962164620.01935554646040.187538781096.96807627011-35.6134694319-7.81934975282
91.57606392230.07212652378131.018117530510.6743329954680.03654854862641.39853621084-0.07383288643140.05356792687050.1859614929270.0420928217108-0.018778537222-0.254809860344-0.2789357950310.176090756350.04698685334450.303839265117-0.07714692256320.02993027766630.1918307441660.02197080099430.30448254788420.3918708704-35.3559399673-4.15096111132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 190 )
9X-RAY DIFFRACTION9chain 'A' and (resid 191 through 208 )

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