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- PDB-5yb6: L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 -... -

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Basic information

Entry
Database: PDB / ID: 5yb6
TitleL-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-lysine complex
ComponentsL-amino acid oxidase/monooxygenase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase/monooxygenase / flavin-containing monoamine oxidase family / flavin monooxygenases / L-lysine
Function / homologytryptophan 2-monooxygenase / Amine oxidase / Flavin containing amine oxidoreductase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / LYSINE / Chem-PG6 / Tryptophan 2-monooxygenase
Function and homology information
Biological speciesPseudomonas sp. AIU 813 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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)263,45320
Polymers258,0674
Non-polymers5,38516
Water18,4831026
1
A: L-amino acid oxidase/monooxygenase
C: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,72610
Polymers129,0342
Non-polymers2,6938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-13.9 kcal/mol
Surface area36820 Å2
MethodPISA
2
B: L-amino acid oxidase/monooxygenase
D: L-amino acid oxidase/monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,72610
Polymers129,0342
Non-polymers2,6938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-15.3 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.071, 132.293, 100.963
Angle α, β, γ (deg.)90.000, 108.670, 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(0.370748, -0.000995, -0.928733), (-0.001479, -0.999999, 0.000481), (-0.928732, 0.001195, -0.370749)32.411491, 7.00297, 47.826031
3given(-0.62427, -0.541875, 0.562723), (-0.543524, -0.216129, -0.811092), (0.561131, -0.812194, -0.159599)10.20826, 32.434959, 24.492929
4given(-0.753666, 0.543171, 0.370071), (0.551177, 0.215598, 0.806053), (0.358038, 0.811469, -0.461873)13.11215, -25.44978, 29.36027

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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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O6
#4: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1026 / 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: 48.32 %
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: 2.1→50 Å / Num. obs: 139347 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.126 / Χ2: 1.008 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.143.30.35168910.637199.7
2.14-2.183.30.33669590.648199.7
2.18-2.223.30.3169720.678199.6
2.22-2.263.40.29769410.73199.7
2.26-2.313.40.27369840.734199.6
2.31-2.373.40.26469380.756199.7
2.37-2.423.40.24769390.815199.7
2.42-2.493.40.22169650.864199.7
2.49-2.563.40.21269620.875199.8
2.56-2.653.40.19869940.914199.8
2.65-2.743.50.18469700.928199.8
2.74-2.853.50.16269780.988199.7
2.85-2.983.50.14669931.072199.7
2.98-3.143.40.1369641.118199.5
3.14-3.333.40.11669421.24199.4
3.33-3.593.40.10270031.381199.4
3.59-3.953.40.09369341.545199.3
3.95-4.523.30.08269631.664199.1
4.52-5.73.40.06770031.173199
5.7-503.50.06870521.36198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WE0

3we0


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 6.978 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 6938 5 %RANDOM
Rwork0.2344 ---
obs0.2369 132300 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.09 Å2 / Biso mean: 19.388 Å2 / Biso min: 2.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17432 0 284 1026 18742
Biso mean--19.64 19.47 -
Num. residues----2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01918316
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216541
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.95724889
X-RAY DIFFRACTIONr_angle_other_deg1.092338321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65252222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8623.429837
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.769152843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5515121
X-RAY DIFFRACTIONr_chiral_restr0.1140.22605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02120403
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023938
Refine LS restraints NCS

Ens-ID: 1 / Number: 8384 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.070.5
2BMEDIUM POSITIONAL0.070.5
3CMEDIUM POSITIONAL0.060.5
4DMEDIUM POSITIONAL0.070.5
1AMEDIUM THERMAL2.382
2BMEDIUM THERMAL2.232
3CMEDIUM THERMAL2.362
4DMEDIUM THERMAL2.182
LS refinement shellResolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 495 -
Rwork0.278 9636 -
all-10131 -
obs--98.16 %

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