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- PDB-5wx2: Crystal structure of porcine kidney D-amino acid oxidase mutant (... -

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Basic information

Entry
Database: PDB / ID: 5wx2
TitleCrystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / OXIDASE / FAD-BINDING
Function / homology
Function and homology information


Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone ...Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / peroxisome / 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 / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMotojima, F. / Yasukawa, K. / Ohno, A. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST, ERATO Japan
CitationJournal: To Be Published
Title: Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine
Authors: Yasukawa, K. / Motojima, F. / Ohno, A. / Asano, Y.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: D-amino-acid oxidase
B: D-amino-acid oxidase
C: D-amino-acid oxidase
D: D-amino-acid oxidase
E: D-amino-acid oxidase
F: D-amino-acid oxidase
G: D-amino-acid oxidase
H: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,34544
Polymers313,8858
Non-polymers9,46136
Water1,26170
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,08413
Polymers78,4712
Non-polymers2,61311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-127 kcal/mol
Surface area27300 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,70710
Polymers78,4712
Non-polymers2,2368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-114 kcal/mol
Surface area27420 Å2
MethodPISA
3
E: D-amino-acid oxidase
F: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,82511
Polymers78,4712
Non-polymers2,3549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-126 kcal/mol
Surface area27540 Å2
MethodPISA
4
G: D-amino-acid oxidase
H: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,72910
Polymers78,4712
Non-polymers2,2588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-108 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.402, 270.896, 135.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-522-

HOH

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Components

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


Mass: 39235.590 Da / Num. of mol.: 8 / Mutation: I230A, R283G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DAO / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00371, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: CCD / Date: Jun 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→49.17 Å / Num. obs: 62192 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rsym value: 0.04 / Net I/σ(I): 15.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.4 / CC1/2: 0.926 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGT

3wgt


Resolution: 3→49.17 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.348 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25335 2943 4.7 %RANDOM
Rwork0.16519 ---
obs0.16945 59226 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.635 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å20 Å2-0 Å2
2--0.03 Å20 Å2
3----4.87 Å2
Refinement stepCycle: 1 / Resolution: 3→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21640 0 630 70 22340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922941
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220745
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.97431345
X-RAY DIFFRACTIONr_angle_other_deg0.97347957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12652711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56823.5331084
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.911153526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.84515160
X-RAY DIFFRACTIONr_chiral_restr0.0770.23352
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02125241
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024923
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_it3.6076.2710832
X-RAY DIFFRACTIONr_mcbond_other3.6076.26910831
X-RAY DIFFRACTIONr_mcangle_it5.8919.413529
X-RAY DIFFRACTIONr_mcangle_other5.899.413530
X-RAY DIFFRACTIONr_scbond_it3.1326.48412108
X-RAY DIFFRACTIONr_scbond_other3.1316.48312105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1629.60217805
X-RAY DIFFRACTIONr_long_range_B_refined8.18169.38725860
X-RAY DIFFRACTIONr_long_range_B_other8.18169.38825861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 219 -
Rwork0.224 4344 -
obs--99.96 %

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