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- PDB-3wgt: Crystal structure of D-amino acid oxidase mutant -

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Basic information

Entry
Database: PDB / ID: 3wgt
TitleCrystal structure of D-amino acid oxidase mutant
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / Oxidase / FAD-binding
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / presynaptic active zone / peroxisomal matrix / digestion / FAD binding / cell projection / peroxisome / extracellular region / cytosol / cytoplasm
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / (1R)-1-phenylethanamine / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYasukawa, K. / Nakano, S. / Asano, Y.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Tailoring D-amino acid oxidase from the pig kidney to R-stereoselective amine oxidase and its use in the deracemization of alpha-methylbenzylamine.
Authors: Yasukawa, K. / Nakano, S. / Asano, Y.
History
DepositionAug 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,65310
Polymers78,4552
Non-polymers2,1988
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-87 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.617, 91.607, 110.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-amino-acid oxidase / DAAO / DAMOX / DAO


Mass: 39227.652 Da / Num. of mol.: 2 / Mutation: Y228L,R283G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DAO / Production host: Escherichia coli (E. coli) / References: UniProt: P00371, D-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: Chemical ChemComp-QSC / (1R)-1-phenylethanamine


Mass: 121.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% Polyethylene glycole 4000, 0.1M TRIS hydrochloride, 0.2M Lithium sulfate monohydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.88→34.13 Å / Num. obs: 56667 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 %
Reflection shellResolution: 1.88→1.91 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AA8

1aa8
PDB Unreleased entry


Resolution: 1.88→34.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.25 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23031 2860 5.1 %RANDOM
Rwork0.18844 ---
all0.19054 56610 --
obs0.19054 53750 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5433 0 144 176 5753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195733
X-RAY DIFFRACTIONr_bond_other_d0.0020.025341
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9767829
X-RAY DIFFRACTIONr_angle_other_deg0.8813.00212239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5115678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24923.582268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.615891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3531540
X-RAY DIFFRACTIONr_chiral_restr0.1590.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216454
X-RAY DIFFRACTIONr_gen_planes_other00.021396
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 195 -
Rwork0.242 3673 -
obs--91.7 %

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