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

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Basic information

Entry
Database: PDB / ID: 5wwv
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


Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / 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
(S)-(4-chlorophenyl)-phenyl-methanamine / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMotojima, F. / Yasukawa, K. / Ohno, A. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST 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 5, 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

Downloads & links

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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)324,31648
Polymers313,8858
Non-polymers10,43140
Water81145
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,06512
Polymers78,4712
Non-polymers2,59410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,02411
Polymers78,4712
Non-polymers2,5539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: D-amino-acid oxidase
F: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,27914
Polymers78,4712
Non-polymers2,80812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: D-amino-acid oxidase
H: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,94711
Polymers78,4712
Non-polymers2,4769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.064, 273.950, 136.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#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

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Non-polymers , 5 types, 85 molecules

#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-7V3 / (S)-(4-chlorophenyl)-phenyl-methanamine


Mass: 217.694 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H12ClN
#4: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.54 Å3/Da / Density % sol: 51.2 % / Description: Rod shaped
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: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→144.49 Å / Num. obs: 52954 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.121 / Net I/σ(I): 13.3
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSJune 17, 2015data reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGT

3wgt


Resolution: 3.2→48.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.898 / SU B: 24.691 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.526 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24212 2657 5 %RANDOM
Rwork0.14494 ---
obs0.14979 50291 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.419 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å2-0 Å2
2--1.14 Å20 Å2
3----4.52 Å2
Refinement stepCycle: 1 / Resolution: 3.2→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21640 0 697 45 22382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01923018
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220728
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.97531443
X-RAY DIFFRACTIONr_angle_other_deg1.022347918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52352709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72523.5331084
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.059153524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.57715160
X-RAY DIFFRACTIONr_chiral_restr0.0860.23353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02125323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024928
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_it5.2797.65710836
X-RAY DIFFRACTIONr_mcbond_other5.2767.65710835
X-RAY DIFFRACTIONr_mcangle_it8.32411.48113536
X-RAY DIFFRACTIONr_mcangle_other8.32411.48213537
X-RAY DIFFRACTIONr_scbond_it5.158.08512182
X-RAY DIFFRACTIONr_scbond_other5.1488.08312179
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.22911.92517899
X-RAY DIFFRACTIONr_long_range_B_refined11.68484.8425861
X-RAY DIFFRACTIONr_long_range_B_other11.68484.84125862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 179 -
Rwork0.225 3673 -
obs--100 %

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