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- PDB-9vpf: Crystal structure of D-aspartate oxidase from Cryptococcus humico... -

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Basic information

Entry
Database: PDB / ID: 9vpf
TitleCrystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.
ComponentsD-aspartate oxidase
KeywordsOXIDOREDUCTASE / D-amino acid
Function / homology
Function and homology information


D-aspartate oxidase / D-aspartate oxidase activity / D-glutamate oxidase activity / D-amino acid catabolic process / nitrogen utilization / cellular detoxification / peroxisomal matrix / FAD binding / peroxisome
Similarity search - Function
D-amino-acid oxidase / FAD dependent oxidoreductase / FAD dependent oxidoreductase
Similarity search - Domain/homology
FLUORIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / D-aspartate oxidase
Similarity search - Component
Biological speciesVanrija humicola (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGoto, M. / Nonaka, R. / Mizobuchi, T. / Imanishi, D. / Takahashi, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP 22770113 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.
Authors: Goto, M. / Nonaka, R. / Mizobuchi, T. / Imanishi, D. / Takahashi, S.
History
DepositionJul 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-aspartate oxidase
B: D-aspartate oxidase
C: D-aspartate oxidase
D: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,19610
Polymers158,0164
Non-polymers3,1806
Water23,4741303
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.983, 109.338, 189.401
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-aspartate oxidase / ChDASPO / ChDDO / DASOX / DASPO / DDO


Mass: 39503.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanrija humicola (fungus) / Strain: UJ1 / Gene: DDO / Plasmid: pET11b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q75WF1, D-aspartate oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 1540, PEG 400, Ammonium Fluoride, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→47.35 Å / Num. obs: 193803 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.074 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.718 / Num. unique obs: 27993 / CC1/2: 0.893 / Rpim(I) all: 0.281 / Rrim(I) all: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.079 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21559 9606 5 %RANDOM
Rwork0.18963 ---
obs0.19093 183666 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.059 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10813 0 214 1303 12330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.96715537
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77851433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.39621.793463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.729151563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.87715112
X-RAY DIFFRACTIONr_chiral_restr0.0860.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218768
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0452.1465744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6363.2157173
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3862.255581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.02619.30919132
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 703 -
Rwork0.264 13432 -
obs--99.97 %

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