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- PDB-3we0: L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 -

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Basic information

Entry
Database: PDB / ID: 3we0
TitleL-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813
ComponentsL-amino acid oxidase/monooxygenase
KeywordsOXIDOREDUCTASE / Flavin-containing monoamine oxidase family / Rossmann Fold / Oxidoreductase (oxidase and monooxygenase)
Function / homology
Function and homology information


lysine 2-monooxygenase / lysine 2-monooxygenase activity / nucleotide binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor; domain 1 - #40 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Guanine Nucleotide Dissociation Inhibitor; domain 1 - #40 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine 2-monooxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsIm, D.H. / Matsui, D. / Fukuta, Y. / Fushinobu, S. / Isobe, K. / Asano, Y.
Citation
Journal: FEBS Open Bio / Year: 2014
Title: Mutational and crystallographic analysis of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813: Interconversion between oxidase and monooxygenase activities
Authors: Matsui, D. / Im, D.H. / Sugawara, A. / Fukuta, Y. / Fushinobu, S. / Isobe, K. / Asano, Y.
#1: Journal: J. Biosci. Bioeng. / Year: 2012
Title: Purification and characterization of an L-amino acid oxidase from Pseudomonas sp. AIU 813
Authors: Isobe, K. / Sugawara, A. / Domon, H. / Fukuta, Y. / Asano, Y.
History
DepositionJun 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-amino acid oxidase/monooxygenase
B: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6054
Polymers129,0342
Non-polymers1,5712
Water7,278404
1
A: L-amino acid oxidase/monooxygenase
B: L-amino acid oxidase/monooxygenase
hetero molecules

A: L-amino acid oxidase/monooxygenase
B: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,2108
Polymers258,0674
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area16100 Å2
ΔGint-58 kcal/mol
Surface area74540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.926, 141.353, 75.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein L-amino acid oxidase/monooxygenase


Mass: 64516.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: AIU 813 / Gene: laao / Plasmid: pET15b-laao / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3IVI6*PLUS, L-amino-acid oxidase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER FOR THIS SEQUENCE IS AB830473.

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 8% polyethylene glycol (PEG) 4000, 0.1M Na-acetate(pH4.6), pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2011
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 101012 / Num. obs: 98486 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 24.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4930 / Rsym value: 0.507 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.38 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25402 4899 5 %RANDOM
Rwork0.20947 ---
obs0.21169 93180 97.02 %-
all-98486 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.149 Å0.156 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8476 0 106 404 8986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_angle_refined_deg2.09
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 337 -
Rwork0.276 6802 -
obs--97.38 %

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