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- PDB-5yb8: L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 -... -

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Basic information

Entry
Database: PDB / ID: 5yb8
TitleL-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-arginine complex
ComponentsL-amino acid oxidase/monooxygenase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase/monooxygenase / flavin-containing monoamine oxidase family / flavin monooxygenases / L-arginine
Function / homology
Function and homology information


tryptophan 2-monooxygenase / monooxygenase activity
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
ARGININE / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 2-monooxygenase
Similarity search - Component
Biological speciesPseudomonas sp. AIU 813 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsIm, D. / Matsui, D. / Arakawa, T. / Isobe, K. / Asano, Y. / Fushinobu, S.
CitationJournal: FEBS Open Bio / Year: 2018
Title: Ligand complex structures of l-amino acid oxidase/monooxygenase from
Authors: Im, D. / Matsui, D. / Arakawa, T. / Isobe, K. / Asano, Y. / Fushinobu, S.
History
DepositionSep 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: 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: L-amino acid oxidase/monooxygenase
B: L-amino acid oxidase/monooxygenase
C: L-amino acid oxidase/monooxygenase
D: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,61116
Polymers258,0674
Non-polymers4,54412
Water5,567309
1
A: L-amino acid oxidase/monooxygenase
D: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3068
Polymers129,0342
Non-polymers2,2726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-24.2 kcal/mol
Surface area38630 Å2
MethodPISA
2
B: L-amino acid oxidase/monooxygenase
C: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3068
Polymers129,0342
Non-polymers2,2726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-29.1 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.200, 133.000, 101.500
Angle α, β, γ (deg.)90.000, 112.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 600
2114B1 - 600
3114C1 - 600
4114D1 - 600

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.769532, 0.517783, 0.373794), (0.518185, 0.164185, 0.839361), (0.373236, 0.83961, -0.394653)12.64397, -25.128189, 26.61482
3given(-0.769532, 0.517783, 0.373794), (0.518185, 0.164185, 0.839361), (0.373236, 0.83961, -0.394653)12.64397, -25.128189, 26.61482
4given(-0.663585, -0.516774, 0.540925), (-0.543251, -0.164242, -0.823348), (0.514327, -0.84022, -0.171749)10.33537, 30.96838, 24.465269

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Components

#1: Protein
L-amino acid oxidase/monooxygenase


Mass: 64516.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. AIU 813 (bacteria) / Gene: laao, mog / Production host: Escherichia coli (E. coli) / References: UniProt: W6JQJ6
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.15M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→94.11 Å / Num. obs: 106954 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.785 % / Biso Wilson estimate: 41.091 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.094 / Χ2: 0.955 / Net I/σ(I): 11.98 / Num. measured all: 404779 / Scaling rejects: 117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.423.8050.4723.24151050.8850.5599.8
2.42-2.673.8070.3164.63234050.9450.36899.8
2.67-3.053.810.1618.09224640.9830.18899.9
3.05-3.853.7930.06915.79230890.9960.08199.8
3.85-103.7250.04424.93215770.9970.05199.4
10-153.6390.0430.869400.9970.04798.5
15-94.113.3160.0428.143740.9980.04789.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata processing
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WE0

3we0


Resolution: 2.3→94.11 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.553 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.261
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 2009 1.9 %RANDOM
Rwork0.2198 ---
obs0.2208 104920 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.94 Å2 / Biso mean: 36.168 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.3→94.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17220 0 212 309 17741
Biso mean--25.96 28.45 -
Num. residues----2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01918032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216648
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.95524532
X-RAY DIFFRACTIONr_angle_other_deg0.872338284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39952192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92123.333828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85152808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.06715124
X-RAY DIFFRACTIONr_chiral_restr0.0940.22580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024308
Refine LS restraints NCS

Ens-ID: 1 / Number: 8411 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.250.5
2BMEDIUM POSITIONAL0.130.5
3CMEDIUM POSITIONAL0.130.5
4DMEDIUM POSITIONAL0.290.5
1AMEDIUM THERMAL9.222
2BMEDIUM THERMAL3.452
3CMEDIUM THERMAL3.452
4DMEDIUM THERMAL42
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 142 -
Rwork0.318 7756 -
all-7898 -
obs--99.82 %

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