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- PDB-5yb7: L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 -... -

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Basic information

Entry
Database: PDB / ID: 5yb7
TitleL-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine complex
ComponentsL-amino acid oxidase/monooxygenase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase/monooxygenase / flavin-containing monoamine oxidase family / flavin monooxygenases / L-ornithine
Function / homology
Function and homology information


tryptophan 2-monooxygenase / auxin biosynthetic process / 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 ...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 / L-ornithine / Tryptophan 2-monooxygenase
Similarity search - Component
Biological speciesPseudomonas sp. AIU 813 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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)262,26716
Polymers258,0674
Non-polymers4,19912
Water14,268792
1
A: L-amino acid oxidase/monooxygenase
C: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1338
Polymers129,0342
Non-polymers2,1006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-27.5 kcal/mol
Surface area37100 Å2
MethodPISA
2
B: L-amino acid oxidase/monooxygenase
D: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1338
Polymers129,0342
Non-polymers2,1006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-28 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 132.900, 101.900
Angle α, β, γ (deg.)90.000, 111.500, 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
1112A1 - 600
2112B1 - 600
3112C1 - 600
4112D1 - 600

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.47269, 0.00365, -0.881222), (0.00359, -0.999991, -0.002216), (-0.881222, -0.002116, -0.472698)28.41823, -8.42104, 47.502399
3given(-0.688317, 0.505702, 0.520082), (0.497168, -0.193219, 0.845867), (0.528247, 0.840792, -0.118423)16.64119, -32.232811, 20.887239
4given(-0.782447, -0.508546, 0.359385), (-0.510341, 0.192973, -0.838041), (0.356831, -0.839132, -0.410523)17.48921, 23.76466, 23.15801

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.15 M 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→94.81 Å / Num. obs: 156339 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.779 % / Biso Wilson estimate: 37.122 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 0.951 / Net I/σ(I): 16.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.153.7460.4073.7300600.9170.47498
2.15-2.323.8130.2545.8256440.9650.29699
2.32-2.553.8150.1548.87246960.9860.1899.1
2.55-2.923.8070.08913.89252430.9940.10499.3
2.92-3.683.7830.04325.08253090.9980.05199.5
3.68-103.7240.02640.55241240.9990.03199.3
10-153.6740.01848.949180.9990.02198.4
15-94.813.3880.02145.363450.9990.02584.8

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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→94.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.285 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 2015 1.4 %RANDOM
Rwork0.1979 ---
obs0.1985 144806 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.65 Å2 / Biso mean: 36.414 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→94.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17220 0 275 792 18287
Biso mean--31.9 35.3 -
Num. residues----2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01918021
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216641
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.95624519
X-RAY DIFFRACTIONr_angle_other_deg0.988338289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47952194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10423.459821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.104152785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.69415116
X-RAY DIFFRACTIONr_chiral_restr0.1010.22581
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02120385
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024283
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A5186MEDIUM POSITIONAL0.040.5
2B5186MEDIUM POSITIONAL0.040.5
3C5186MEDIUM POSITIONAL0.040.5
4D5186MEDIUM POSITIONAL0.040.5
1A3205TIGHT THERMAL70.5
2B3205TIGHT THERMAL6.890.5
3C3205TIGHT THERMAL6.380.5
4D3205TIGHT THERMAL7.690.5
1A5186MEDIUM THERMAL7.322
2B5186MEDIUM THERMAL7.22
3C5186MEDIUM THERMAL6.752
4D5186MEDIUM THERMAL8.092
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 135 -
Rwork0.291 9482 -
all-9617 -
obs--82.61 %

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