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- PDB-6gg2: The structure of FsqB from Aspergillus fumigatus, a flavoenzyme o... -

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Basic information

Entry
Database: PDB / ID: 6gg2
TitleThe structure of FsqB from Aspergillus fumigatus, a flavoenzyme of the amine oxidase family
ComponentsAmino acid oxidase fmpA
KeywordsOXIDOREDUCTASE / flavoenzyme / amine oxidase family
Function / homology
Function and homology information


L-pipecolate oxidase activity / Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / sarcosine oxidase activity / proline dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Amino acid oxidase fsqB
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsPavkov-Keller, T. / Lahham, M. / Macheroux, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Oxidative cyclization ofN-methyl-dopa by a fungal flavoenzyme of the amine oxidase family.
Authors: Lahham, M. / Pavkov-Keller, T. / Fuchs, M. / Niederhauser, J. / Chalhoub, G. / Daniel, B. / Kroutil, W. / Gruber, K. / Macheroux, P.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

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Assembly

Deposited unit
A: Amino acid oxidase fmpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7772
Polymers54,9921
Non-polymers7861
Water64936
1
A: Amino acid oxidase fmpA
hetero molecules

A: Amino acid oxidase fmpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5554
Polymers109,9842
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7250 Å2
ΔGint-39 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.123, 90.123, 266.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Amino acid oxidase fmpA / Fumipyrrole biosynthesis protein A


Mass: 54991.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: fmpA, AFUA_6G03440 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WD43, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.26 M ammonium sulphate, 0.2 M lithium sulphate, 0.1 M TrisHCL, pH 8.5 protein concentrations of 10, 20 and 30 mg mL-1 in 100 mM phosphate/NaOH pH 7.8 and 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 20505 / % possible obs: 98.9 % / Redundancy: 15.4 % / CC1/2: 1 / Rmerge(I) obs: 0.0827 / Rpim(I) all: 0.0218 / Rrim(I) all: 0.0856 / Net I/σ(I): 24.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.7854 / Num. unique obs: 1862 / CC1/2: 0.95 / Rpim(I) all: 0.2039 / Rrim(I) all: 0.8121 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DJE

3dje


Resolution: 2.598→45.062 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1022 5 %
Rwork0.2123 --
obs0.2138 20430 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→45.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 0 36 3945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044009
X-RAY DIFFRACTIONf_angle_d0.8125466
X-RAY DIFFRACTIONf_dihedral_angle_d11.8282367
X-RAY DIFFRACTIONf_chiral_restr0.047597
X-RAY DIFFRACTIONf_plane_restr0.005711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5982-2.73520.30381370.25512585X-RAY DIFFRACTION95
2.7352-2.90650.33961430.26952730X-RAY DIFFRACTION100
2.9065-3.13090.35031440.28092731X-RAY DIFFRACTION100
3.1309-3.44580.37181450.25552752X-RAY DIFFRACTION100
3.4458-3.94420.241440.22362727X-RAY DIFFRACTION98
3.9442-4.96830.18991500.18032844X-RAY DIFFRACTION100
4.9683-45.06830.2041590.18843039X-RAY DIFFRACTION100

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