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- PDB-5m1e: Crystal structure of N-terminally tagged UbiD from E. coli recons... -

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Basic information

Entry
Database: PDB / ID: 5m1e
TitleCrystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN cofactor
Components3-octaprenyl-4-hydroxybenzoate carboxy-lyase
KeywordsLYASE / UbiD / decarboxylase / ubiquinone biosynthesis / prFMN binding
Function / homology
Function and homology information


4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
UbiD decarboxylyase, bacteria / UbiD C-terminal domain-like / UbiD C-terminal domain-like / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain ...UbiD decarboxylyase, bacteria / UbiD C-terminal domain-like / UbiD C-terminal domain-like / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7D9 / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å
AuthorsMarshall, S.A. / Leys, D.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Authors: Marshall, S.A. / Fisher, K. / Ni Cheallaigh, A. / White, M.D. / Payne, K.A. / Parker, D.A. / Rigby, S.E. / Leys, D.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jan 17, 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_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,56412
Polymers173,5113
Non-polymers2,0539
Water2,342130
1
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules

A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,12824
Polymers347,0216
Non-polymers4,10718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area33600 Å2
ΔGint-271 kcal/mol
Surface area96730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.520, 194.520, 107.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-653-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA6 - 49126 - 511
21TYRTYRBB6 - 49126 - 511
12ASNASNAA7 - 49127 - 511
22ASNASNCC7 - 49127 - 511
13ASNASNBB7 - 49127 - 511
23ASNASNCC7 - 49127 - 511

NCS ensembles :
ID
1
2
3

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Components

#1: Protein 3-octaprenyl-4-hydroxybenzoate carboxy-lyase / Polyprenyl p-hydroxybenzoate decarboxylase


Mass: 57836.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: ubiD, c4790 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAB5, 4-hydroxy-3-polyprenylbenzoate decarboxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-7D9 / (16~{R})-11,12,14,14-tetramethyl-3,5-bis(oxidanylidene)-8-[(2~{S},3~{S},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),9(17),10,12-tetraene-16-sulfonic acid


Mass: 606.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H31N4O12PS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 mM SPG pH 8, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.044 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.62→94.03 Å / Num. obs: 58691 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.7
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5M1C

5m1c


Resolution: 2.62→94.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.564 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21182 3085 5 %RANDOM
Rwork0.17545 ---
obs0.17723 58691 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.207 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.62→94.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10906 0 126 130 11162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911314
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210707
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9815441
X-RAY DIFFRACTIONr_angle_other_deg1.261324655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23651386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04623.891496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.895151806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931577
X-RAY DIFFRACTIONr_chiral_restr0.1110.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112660
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022476
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A270680.11
12B270680.11
21A254620.13
22C254620.13
31B260390.11
32C260390.11
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 232 -
Rwork0.315 4292 -
obs--99.98 %
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)
11.55650.4551-0.16891.5106-0.51110.57670.1235-0.9570.37840.234-0.17980.0975-0.12250.05210.05630.111-0.0418-0.00030.7182-0.2930.13915.646-18.5751.312
21.17380.6502-0.18422.36650.28931.51690.0652-0.08360.23030.1182-0.0618-0.1037-0.1154-0.0423-0.00340.02150.0124-0.02620.08-0.06670.220578.548-14.414-9.064
31.2672-0.7130.31892.2717-0.56551.73060.17080.12540.0452-0.1694-0.1591-0.20130.09420.115-0.01170.1362-0.0139-0.00210.06220.0280.059865.413-70.2594.57
40.4583-0.16150.06670.40590.06840.4778-0.0398-0.14440.096-0.01720.003-0.0353-0.00530.0660.03690.11170.01680.00710.1372-0.01030.112249.848-35.405-16.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 330
2X-RAY DIFFRACTION1C471 - 550
3X-RAY DIFFRACTION2A1 - 330
4X-RAY DIFFRACTION2B471 - 550
5X-RAY DIFFRACTION3B1 - 330
6X-RAY DIFFRACTION3A471 - 550
7X-RAY DIFFRACTION4A331 - 470
8X-RAY DIFFRACTION4B331 - 470
9X-RAY DIFFRACTION4C331 - 470

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