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- PDB-5o8r: The crystal structure of DfoA bound to FAD and NADP; the desferri... -

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Basic information

Entry
Database: PDB / ID: 5o8r
TitleThe crystal structure of DfoA bound to FAD and NADP; the desferrioxamine biosynthetic pathway cadaverine monooxygenase from the fire blight disease pathogen Erwinia amylovora
ComponentsL-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
KeywordsBIOSYNTHETIC PROTEIN / siderophore biosynthesis / cadaverine monooxygenase / NADP(H) / FAD
Function / homologyL-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
Function and homology information
Biological speciesErwinia amylovora CFBP1430 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 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 14, 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
B: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9176
Polymers100,8592
Non-polymers3,0584
Water1,45981
1
A: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
hetero molecules

A: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
hetero molecules

B: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
hetero molecules

B: L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,83512
Polymers201,7194
Non-polymers6,1168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area31890 Å2
ΔGint-142 kcal/mol
Surface area62460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.937, 163.937, 166.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis


Mass: 50429.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia amylovora CFBP1430 (bacteria) / Gene: dfoA, EAMY_3239 / Production host: Escherichia coli (E. coli)
References: UniProt: D4I246, L-lysine N6-monooxygenase (NADPH)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 5.58 Å3/Da / Density % sol: 77.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES, 1.3 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→47.59 Å / Num. obs: 56459 / % possible obs: 99.81 % / Redundancy: 8.8 % / Rrim(I) all: 0.146 / Net I/σ(I): 16.3
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 2 / Rrim(I) all: 1.295

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.905 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23969 2895 5.1 %RANDOM
Rwork0.18732 ---
obs0.19001 53499 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 202 81 7319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197502
X-RAY DIFFRACTIONr_bond_other_d0.0030.026550
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.97610222
X-RAY DIFFRACTIONr_angle_other_deg1.166315194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21223.673392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.808151217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7891555
X-RAY DIFFRACTIONr_chiral_restr0.1090.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021668
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_it5.2455.9913439
X-RAY DIFFRACTIONr_mcbond_other5.2325.993438
X-RAY DIFFRACTIONr_mcangle_it7.9158.9854304
X-RAY DIFFRACTIONr_mcangle_other7.9158.9864305
X-RAY DIFFRACTIONr_scbond_it6.4756.74062
X-RAY DIFFRACTIONr_scbond_other6.4756.7024063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.9149.8645918
X-RAY DIFFRACTIONr_long_range_B_refined13.69470.1038854
X-RAY DIFFRACTIONr_long_range_B_other13.770.1158853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 195 -
Rwork0.356 3872 -
obs--98.93 %

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