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- PDB-7abo: Structure of the N318H variant of the reversible pyrrole-2-carbox... -

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Basic information

Entry
Database: PDB / ID: 7abo
TitleStructure of the N318H variant of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA in complex with FMN
ComponentsUbiD-like decarboxylase
KeywordsLIGASE / prFMN / decarboxylase / UbiD / pyrrole / pyrrole-2-carboxylic acid
Function / homology
Function and homology information


: / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / metal ion binding
Similarity search - Function
UbiD-like decarboxylase/ferulic acid decarboxylase 1 / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / UbiD-like decarboxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeys, D. / Marshall, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ADG_695013 United Kingdom
CitationJournal: Acs Catalysis / Year: 2021
Title: Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence.
Authors: Payne, K.A.P. / Marshall, S.A. / Fisher, K. / Rigby, S.E.J. / Cliff, M.J. / Spiess, R. / Cannas, D.M. / Larrosa, I. / Hay, S. / Leys, D.
History
DepositionSep 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: UbiD-like decarboxylase
B: UbiD-like decarboxylase
D: UbiD-like decarboxylase
A: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,94216
Polymers219,8054
Non-polymers2,13712
Water19,0961060
1
C: UbiD-like decarboxylase
B: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9718
Polymers109,9032
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-88 kcal/mol
Surface area32540 Å2
MethodPISA
2
D: UbiD-like decarboxylase
A: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9718
Polymers109,9032
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-92 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.880, 55.570, 198.880
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UbiD-like decarboxylase / Ferulic acid decarboxylase-like protein


Mass: 54951.262 Da / Num. of mol.: 4 / Mutation: N318H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ECC04_013425 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5F1BUV8, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M amino acids, 0.1 M NaHEPES/MOPS buffer pH 7.5, 20% v/v glycerol and 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→47.75 Å / Num. obs: 168873 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 1 / Rrim(I) all: 0.081 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8399 / CC1/2: 0.5 / Rrim(I) all: 1.025 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWS

4iws


Resolution: 1.95→40.928 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 8445 5 %
Rwork0.2144 --
obs0.216 168830 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→40.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15283 0 132 1060 16475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415851
X-RAY DIFFRACTIONf_angle_d0.68221691
X-RAY DIFFRACTIONf_dihedral_angle_d7.4399279
X-RAY DIFFRACTIONf_chiral_restr0.0472358
X-RAY DIFFRACTIONf_plane_restr0.0042862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.35392580.32735309X-RAY DIFFRACTION99
1.9722-1.99540.33852440.31285353X-RAY DIFFRACTION99
1.9954-2.01970.35052550.30735354X-RAY DIFFRACTION100
2.0197-2.04530.32962850.28935324X-RAY DIFFRACTION100
2.0453-2.07220.31792860.29485311X-RAY DIFFRACTION99
2.0722-2.10060.33372920.28715286X-RAY DIFFRACTION100
2.1006-2.13060.29792890.28195403X-RAY DIFFRACTION99
2.1306-2.16240.33163120.27395269X-RAY DIFFRACTION100
2.1624-2.19620.27942760.27015300X-RAY DIFFRACTION100
2.1962-2.23220.3122730.2515364X-RAY DIFFRACTION100
2.2322-2.27070.28043080.24135244X-RAY DIFFRACTION99
2.2707-2.31190.27092910.23435419X-RAY DIFFRACTION100
2.3119-2.35640.2812650.2375262X-RAY DIFFRACTION100
2.3564-2.40450.2852940.23645392X-RAY DIFFRACTION100
2.4045-2.45680.28622870.22915356X-RAY DIFFRACTION100
2.4568-2.51390.27372740.22265389X-RAY DIFFRACTION100
2.5139-2.57680.27122610.22555339X-RAY DIFFRACTION100
2.5768-2.64640.26772970.21975390X-RAY DIFFRACTION100
2.6464-2.72430.26412430.2255325X-RAY DIFFRACTION100
2.7243-2.81220.26982630.22395415X-RAY DIFFRACTION100
2.8122-2.91270.24972950.2195327X-RAY DIFFRACTION99
2.9127-3.02930.24113120.215320X-RAY DIFFRACTION99
3.0293-3.16710.23862850.21425341X-RAY DIFFRACTION99
3.1671-3.3340.22432740.215334X-RAY DIFFRACTION99
3.334-3.54280.21862920.19915360X-RAY DIFFRACTION99
3.5428-3.81610.21512630.19445333X-RAY DIFFRACTION98
3.8161-4.19980.24053130.18935321X-RAY DIFFRACTION98
4.1998-4.80670.1882720.17315351X-RAY DIFFRACTION98
4.8067-6.05280.22652950.195392X-RAY DIFFRACTION98
6.0528-40.9280.21812910.19375502X-RAY DIFFRACTION97

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