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- PDB-5o5c: The crystal structure of DfoJ, the desferrioxamine biosynthetic p... -

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Basic information

Entry
Database: PDB / ID: 5o5c
TitleThe crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora
ComponentsPutative decarboxylase involved in desferrioxamine biosynthesis
KeywordsLYASE / siderophore biosynthesis / E.C. 4.1.1.18 / group II PLP-dependent enzyme / aspartate aminotransferase family type 1 fold subclass II
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Putative decarboxylase involved in desferrioxamine biosynthesis
Similarity search - Component
Biological speciesErwinia amylovora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSalomone-Stagni, M. / Bartho, J.D. / Polsinelli, I. / Bellini, D. / Walsh, M.A. / Demitri, N. / Benini, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Autonomous province of Bolzanovirelunce and pathogenesys of Erwinia amylovora Italy
CitationJournal: J. Struct. Biol. / Year: 2018
Title: A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora.
Authors: Salomone-Stagni, M. / Bartho, J.D. / Polsinelli, I. / Bellini, D. / Walsh, M.A. / Demitri, N. / Benini, S.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
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
A: Putative decarboxylase involved in desferrioxamine biosynthesis
B: Putative decarboxylase involved in desferrioxamine biosynthesis
C: Putative decarboxylase involved in desferrioxamine biosynthesis
D: Putative decarboxylase involved in desferrioxamine biosynthesis
E: Putative decarboxylase involved in desferrioxamine biosynthesis
F: Putative decarboxylase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,17512
Polymers341,6926
Non-polymers1,4836
Water3,603200
1
A: Putative decarboxylase involved in desferrioxamine biosynthesis
B: Putative decarboxylase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3924
Polymers113,8972
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-87 kcal/mol
Surface area30930 Å2
MethodPISA
2
C: Putative decarboxylase involved in desferrioxamine biosynthesis
D: Putative decarboxylase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3924
Polymers113,8972
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-83 kcal/mol
Surface area30790 Å2
MethodPISA
3
E: Putative decarboxylase involved in desferrioxamine biosynthesis
hetero molecules

F: Putative decarboxylase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3924
Polymers113,8972
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area13410 Å2
ΔGint-85 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.791, 269.791, 56.194
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Putative decarboxylase involved in desferrioxamine biosynthesis


Mass: 56948.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia amylovora (strain CFBP1430) (bacteria)
Strain: CFBP1430 / Gene: dfoJ, EAMY_3238 / Production host: Escherichia coli (E. coli)
References: UniProt: D4I245, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 55% V/V polipropylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→74.96 Å / Num. obs: 134700 / % possible obs: 99.91 % / Redundancy: 8.1 % / Rpim(I) all: 0.084 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 3.8 / Rpim(I) all: 0.633

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMA

2qma


Resolution: 2.1→233.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.068 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18662 13243 5 %RANDOM
Rwork0.16496 ---
obs0.16604 253433 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.476 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→233.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21713 0 90 200 22003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01922306
X-RAY DIFFRACTIONr_bond_other_d0.0030.0220610
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.94430299
X-RAY DIFFRACTIONr_angle_other_deg1.158347660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68452762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56723.704988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.595153653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1115131
X-RAY DIFFRACTIONr_chiral_restr0.1140.23439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02124728
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024543
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_it2.6162.87211120
X-RAY DIFFRACTIONr_mcbond_other2.6162.87211119
X-RAY DIFFRACTIONr_mcangle_it3.6554.29413858
X-RAY DIFFRACTIONr_mcangle_other3.6554.29413859
X-RAY DIFFRACTIONr_scbond_it3.2643.28111186
X-RAY DIFFRACTIONr_scbond_other3.2643.28111187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7514.80216442
X-RAY DIFFRACTIONr_long_range_B_refined6.75735.09625073
X-RAY DIFFRACTIONr_long_range_B_other6.75735.08425065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.127 1042 -
Rwork0.099 18582 -
obs--98.94 %

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