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- PDB-5m1b: Crystal structure of C-terminally tagged apo-UbiD from E. coli -

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Basic information

Entry
Database: PDB / ID: 5m1b
TitleCrystal structure of C-terminally tagged apo-UbiD from E. coli
Components3-octaprenyl-4-hydroxybenzoate carboxy-lyase
KeywordsLYASE / UbiD / decarboxylase / ubiquinone biosynthesis / prFMN binding
Function / homology
Function and homology information


4-hydroxy-3-polyprenylbenzoate decarboxylase / 4-hydroxy-3-polyprenylbenzoate decarboxylase activity / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Single helix bin / 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 ...Single helix bin / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsWhite, M. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802/1 United Kingdom
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 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)170,2103
Polymers170,2103
Non-polymers00
Water00
1
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase

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


Theoretical massNumber of molelcules
Total (without water)340,4206
Polymers340,4206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area31710 Å2
ΔGint-157 kcal/mol
Surface area100650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.187, 210.187, 109.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILEAA8 - 4908 - 490
21ASPASPILEILEBB8 - 4908 - 490
12ASPASPPHEPHEAA8 - 4918 - 491
22ASPASPPHEPHECC8 - 4918 - 491
13ASNASNILEILEBB7 - 4907 - 490
23ASNASNILEILECC7 - 4907 - 490

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 56736.629 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)
Gene: ubiD, c4790 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAB5, 4-hydroxy-3-polyprenylbenzoate decarboxylase

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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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Crystals grown in 0.1 mM SPG pH 8, 25 w/v PEG 1500 Crystals were cryo-protected using 10 PEG 400 in mother liquor followed by rapid cryocooling.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.044 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 3.15→29.9 Å / Num. obs: 51401 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 14.1
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IDB

2idb


Resolution: 3.15→29.9 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU B: 52.237 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27655 2155 5 %RANDOM
Rwork0.22103 ---
obs0.22384 40600 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.991 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å2-0 Å2-0 Å2
2---5.62 Å20 Å2
3---11.23 Å2
Refinement stepCycle: 1 / Resolution: 3.15→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10593 0 0 0 10593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.96514791
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17851340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62323.897485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.772151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4091575
X-RAY DIFFRACTIONr_chiral_restr0.1050.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218302
X-RAY DIFFRACTIONr_gen_planes_other
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)
11A4880.15
12B4880.15
21A4990.15
22C4990.15
31B4990.13
32C4990.13
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 142 -
Rwork0.295 2964 -
obs--100 %
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)
11.967-0.1674-0.18430.3585-0.46370.952-0.1122-0.54250.3520.1451-0.0319-0.0291-0.1053-0.10350.1440.1531-0.05750.09850.4156-0.26090.249-75.061563.1104-1.7213
22.08540.3407-0.15562.25920.01081.32020.2027-0.27410.54680.3304-0.0851-0.2595-0.2163-0.2223-0.11760.21750.047-0.05240.3459-0.20420.3073-5.880466.1404-2.9342
32.09-1.5309-0.53411.7415-0.1751.57740.1677-0.54-0.63070.2115-0.18720.187-0.01870.4130.01950.8729-0.2567-0.53690.79880.44710.5345-22.21639.50832.4392
41.52590.46550.52121.48510.2570.79560.1667-0.1920.25550.2831-0.1030.10690.26570.1383-0.06370.26620.01960.00740.3023-0.0710.0858-35.314947.1606-15.2261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C7 - 330
2X-RAY DIFFRACTION1C471 - 491
3X-RAY DIFFRACTION2A8 - 330
4X-RAY DIFFRACTION2B471 - 490
5X-RAY DIFFRACTION3B6 - 330
6X-RAY DIFFRACTION3A471 - 491
7X-RAY DIFFRACTION4A331 - 470
8X-RAY DIFFRACTION4B331 - 470
9X-RAY DIFFRACTION4C331 - 470

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