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- PDB-4zaf: Structure of UbiX in complex with oxidised FMN and dimethylallyl ... -

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Basic information

Entry
Database: PDB / ID: 4zaf
TitleStructure of UbiX in complex with oxidised FMN and dimethylallyl monophosphate
ComponentsProbable aromatic acid decarboxylase
KeywordsLYASE / prenyl transferase / flavin binding / UbiX
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / prenyltransferase activity / carboxy-lyase 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 / FOURIER SYNTHESIS / Resolution: 1.71 Å
AuthorsWhite, M.D. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
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 1.2Aug 30, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable aromatic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2798
Polymers22,3851
Non-polymers8947
Water2,504139
1
A: Probable aromatic acid decarboxylase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)279,34396
Polymers268,61712
Non-polymers10,72784
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 area71860 Å2
ΔGint-413 kcal/mol
Surface area68830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.900, 141.900, 141.900
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-501-

HOH

21A-518-

HOH

31A-521-

HOH

41A-532-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable aromatic acid decarboxylase


Mass: 22384.740 Da / Num. of mol.: 1
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, 146 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.: 4 / 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.: 139 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
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: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.71→70.95 Å / Num. obs: 24314 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 18.7
Reflection shellResolution: 1.71→1.75 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: This structure was solved using difference fourier

Resolution: 1.71→70.95 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.77 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17231 1295 5.1 %RANDOM
Rwork0.13744 ---
obs0.1392 24314 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.416 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.71→70.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 54 139 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021712
X-RAY DIFFRACTIONr_bond_other_d0.0020.021652
X-RAY DIFFRACTIONr_angle_refined_deg2.1192.0012342
X-RAY DIFFRACTIONr_angle_other_deg0.9963.0063795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35323.88167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051513
X-RAY DIFFRACTIONr_chiral_restr0.2850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02375
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_it2.2572.093871
X-RAY DIFFRACTIONr_mcbond_other2.2562.094872
X-RAY DIFFRACTIONr_mcangle_it3.0543.1171094
X-RAY DIFFRACTIONr_mcangle_other3.0533.1181095
X-RAY DIFFRACTIONr_scbond_it3.4722.46841
X-RAY DIFFRACTIONr_scbond_other3.4612.454836
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1613.541242
X-RAY DIFFRACTIONr_long_range_B_refined6.48918.5512075
X-RAY DIFFRACTIONr_long_range_B_other6.48818.5592076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.755 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 88 -
Rwork0.211 1773 -
obs--99.95 %

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