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- PDB-4yjh: Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrroli... -

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Basic information

Entry
Database: PDB / ID: 4yjh
TitleCrystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form)
Components(D-amino-acid ...) x 2
KeywordsOXIDOREDUCTASE / amine oxidase / Variant of D-amino acid oxidase / R-2-phenylpyrrolidine binding form
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 / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / 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 oxidases signature. / D-amino-acid oxidase / 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
(2R)-2-phenylpyrrolidine / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNakano, S. / Yasukawa, K. / Kawahara, N. / Ishitsubo, E. / Tokiwa, H. / Asano, Y.
CitationJournal: To Be Published
Title: Crystal structure of DAAO variant
Authors: Nakano, S. / Yasukawa, K. / Kawahara, N. / Ishitsubo, E. / Tokiwa, H. / Asano, Y.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2219
Polymers77,0682
Non-polymers2,1547
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-71 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.281, 91.202, 110.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 339 / Label seq-ID: 1 - 339

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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D-amino-acid ... , 2 types, 2 molecules AB

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


Mass: 38604.902 Da / Num. of mol.: 1 / Fragment: UNP residues 1-340 / 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: Protein D-amino-acid oxidase / DAO


Mass: 38462.746 Da / Num. of mol.: 1 / Fragment: UNP residues 1-340 / 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

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Non-polymers , 4 types, 24 molecules

#3: Chemical ChemComp-96B / (2R)-2-phenylpyrrolidine


Mass: 147.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.1MTris-HCl(8.5), 0.2M Lithium sulfate

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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 315r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→47.1 Å / Num. obs: 19402 / % possible obs: 98.4 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 36.8
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 8 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGT

3wgt


Resolution: 2.7→47.1 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.34 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 991 5.1 %RANDOM
Rwork0.19239 ---
obs0.19601 18348 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.282 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 143 17 5605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195747
X-RAY DIFFRACTIONr_bond_other_d0.0020.025362
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9767848
X-RAY DIFFRACTIONr_angle_other_deg0.743312292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81923.582268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78515892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7051540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021398
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 20491 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 51 -
Rwork0.244 1219 -
obs--90.01 %

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