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- PDB-5o7o: The crystal structure of DfoC, the desferrioxamine biosynthetic p... -

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Basic information

Entry
Database: PDB / ID: 5o7o
TitleThe crystal structure of DfoC, the desferrioxamine biosynthetic pathway acetyltransferase/Non-Ribosomal Peptide Synthetase (NRPS)-Independent Siderophore (NIS) from the fire blight disease pathogen Erwinia amylovora
ComponentsDesferrioxamine siderophore biosynthesis protein dfoC
KeywordsBIOSYNTHETIC PROTEIN / siderophore biosynthesis / desferrioxamine / fire blight
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / acyltransferase activity
Similarity search - Function
Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Acyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter ...Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Acyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / Acetyltransferase (GNAT) domain / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Acyl-CoA N-acyltransferase / Helix non-globular / Special / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Desferrioxamine siderophore biosynthesis protein dfoC
Similarity search - Component
Biological speciesErwinia amylovora CFBP1430 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSalomone-Stagni, M. / Bartho, J.D. / Polsinelli, I. / Bellini, D. / Walsh, M.A. / Demitri, N. / Benini, S.
Funding support Italy, 2items
OrganizationGrant numberCountry
Autonomous Province of Bolzano Italy
Free University of Bolzano 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 9, 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: Desferrioxamine siderophore biosynthesis protein dfoC
B: Desferrioxamine siderophore biosynthesis protein dfoC
C: Desferrioxamine siderophore biosynthesis protein dfoC
D: Desferrioxamine siderophore biosynthesis protein dfoC


Theoretical massNumber of molelcules
Total (without water)359,6284
Polymers359,6284
Non-polymers00
Water7,656425
1
A: Desferrioxamine siderophore biosynthesis protein dfoC
B: Desferrioxamine siderophore biosynthesis protein dfoC


Theoretical massNumber of molelcules
Total (without water)179,8142
Polymers179,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Desferrioxamine siderophore biosynthesis protein dfoC
D: Desferrioxamine siderophore biosynthesis protein dfoC


Theoretical massNumber of molelcules
Total (without water)179,8142
Polymers179,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.170, 156.350, 93.810
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Desferrioxamine siderophore biosynthesis protein dfoC


Mass: 89907.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DfoC N-terminal domain / Source: (gene. exp.) Erwinia amylovora CFBP1430 (bacteria) / Gene: dfoC, EAMY_3240 / Production host: Escherichia coli (E. coli) / References: UniProt: D4I247
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M TRIS-HCl, 0.2 M MgCl2, 0.06 M Ammonium citrate, 10% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.11→78.18 Å / Num. obs: 123387 / % possible obs: 99.79 % / Redundancy: 3.4 % / Rrim(I) all: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 2.11→2.165 Å / Num. unique obs: 9132

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x0o

2x0o


Resolution: 2.11→78.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.851 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 6119 5 %RANDOM
Rwork0.22055 ---
obs0.2227 117229 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-4.14 Å2
2---3.38 Å2-0 Å2
3---4.29 Å2
Refinement stepCycle: 1 / Resolution: 2.11→78.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11584 0 0 425 12009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911888
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210737
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.93516147
X-RAY DIFFRACTIONr_angle_other_deg1.04324857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85351433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28623.802597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.775151937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731578
X-RAY DIFFRACTIONr_chiral_restr0.0980.21745
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022563
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_it3.1895.0575756
X-RAY DIFFRACTIONr_mcbond_other3.1895.0575755
X-RAY DIFFRACTIONr_mcangle_it4.4337.5717181
X-RAY DIFFRACTIONr_mcangle_other4.4327.5717182
X-RAY DIFFRACTIONr_scbond_it3.4315.2756132
X-RAY DIFFRACTIONr_scbond_other3.4315.2766133
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8987.8138967
X-RAY DIFFRACTIONr_long_range_B_refined6.65958.40513227
X-RAY DIFFRACTIONr_long_range_B_other6.64358.33713184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å
RfactorNum. reflection% reflection
Rfree0.34 462 5 %
Rwork0.35 8668 -
obs--99.85 %

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