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- PDB-7abn: Structure of the reversible pyrrole-2-carboxylic acid decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 7abn
TitleStructure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA
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
Chem-4LU / IMIDAZOLE / : / : / UbiD-like decarboxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLeys, D.
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
D: UbiD-like decarboxylase
A: UbiD-like decarboxylase
H: UbiD-like decarboxylase
M: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,01420
Polymers218,2594
Non-polymers2,75416
Water25,6531424
1
D: UbiD-like decarboxylase
M: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,50710
Polymers109,1302
Non-polymers1,3778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-43 kcal/mol
Surface area33020 Å2
MethodPISA
2
A: UbiD-like decarboxylase
H: UbiD-like decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,50710
Polymers109,1302
Non-polymers1,3778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-41 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.810, 55.480, 199.530
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules DAHM

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


Mass: 54564.844 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 1440 molecules

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


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: 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.: 4 / Source method: isolated from a natural source / Formula: C22H30N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1424 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.12 M alcohols, 0.1 M imidazole/MES pH 6.5, 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→54 Å / Num. obs: 279939 / % possible obs: 96.4 % / Redundancy: 3.1 % / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 8.6
Reflection shellResolution: 1.63→1.67 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 18328 / CC1/2: 0.7 / Rrim(I) all: 0.812 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWS

4iws


Resolution: 1.65→53.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.25 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23475 14039 5 %RANDOM
Rwork0.20145 ---
obs0.20311 265205 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.082 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20.4 Å2
2---1.1 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.65→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15347 0 172 1424 16943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01915984
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215022
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9621856
X-RAY DIFFRACTIONr_angle_other_deg1.012334362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7751982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86722.395739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19152339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.99315161
X-RAY DIFFRACTIONr_chiral_restr0.1640.22365
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02118288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023849
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
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 977 -
Rwork0.298 19511 -
obs--99.36 %

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