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- PDB-5m1d: Crystal structure of N-terminally tagged UbiD from E. coli recons... -

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Basic information

Entry
Database: PDB / ID: 5m1d
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


prenyl-FMNH2 binding / 4-hydroxy-3-polyprenylbenzoate decarboxylase / ubiquinone biosynthetic process from chorismate / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / protein hexamerization / manganese ion binding / identical protein binding ...prenyl-FMNH2 binding / 4-hydroxy-3-polyprenylbenzoate decarboxylase / ubiquinone biosynthetic process from chorismate / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / protein hexamerization / manganese ion binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol
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-4LU / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 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 / 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 / struct_conn / struct_ncs_dom_lim
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 / _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)175,41713
Polymers173,5113
Non-polymers1,90610
Water2,432135
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)350,83426
Polymers347,0216
Non-polymers3,81320
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area34000 Å2
ΔGint-329 kcal/mol
Surface area97470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.199, 194.199, 107.598
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-664-

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
3
1
2

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Components

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Protein , 1 types, 3 molecules ABC

#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 (E. coli) / Gene: ubiD, c4790 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAB5, UniProt: P0AAB4*PLUS, 4-hydroxy-3-polyprenylbenzoate decarboxylase

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: 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.: 3 / Source method: obtained synthetically / Formula: C22H30N4O9P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / 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.: 135 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
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: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.7→137.32 Å / Num. obs: 54077 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rsym value: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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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: 2.7→137.32 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 24.269 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.282 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2808 4.9 %RANDOM
Rwork0.195 ---
obs0.196 54077 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→137.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10899 0 119 135 11153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911299
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210698
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.97915413
X-RAY DIFFRACTIONr_angle_other_deg1.19324632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67423.879495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54151803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8031577
X-RAY DIFFRACTIONr_chiral_restr0.1030.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112654
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022474
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)
11A273040.1
12B273040.1
21A259090.11
22C259090.11
31B262950.1
32C262950.1
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 202 -
Rwork0.322 3918 -
obs--99.71 %
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)
12.1460.7868-0.79221.8357-0.56441.42430.336-1.16910.29870.4315-0.3370.138-0.19290.33940.0010.1455-0.1041-0.01340.7609-0.29150.186615.646-18.5751.312
21.30420.9339-0.27772.70610.80921.78390.1348-0.39760.34050.1465-0.2225-0.1035-0.1884-0.11130.08770.113-0.0119-0.06430.3786-0.18190.486378.548-14.414-9.064
31.4241-0.86240.08172.5623-0.74681.97860.14750.10030.003-0.186-0.1406-0.20140.12950.0441-0.00690.0511-0.0005-0.02050.01890.0240.120965.413-70.2594.57
40.5036-0.1120.01860.2576-0.04350.3541-0.0352-0.20430.0841-0.01750-0.0638-0.01820.12590.03520.07390.04810.01070.1577-0.00150.186849.848-35.405-16.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C7 - 330
2X-RAY DIFFRACTION1C471 - 491
3X-RAY DIFFRACTION2A6 - 330
4X-RAY DIFFRACTION2B471 - 491
5X-RAY DIFFRACTION3B6 - 330
6X-RAY DIFFRACTION3A471 - 491
7X-RAY DIFFRACTION4A331 - 470
8X-RAY DIFFRACTION4B331 - 470
9X-RAY DIFFRACTION4C331 - 470

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