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- PDB-7ct4: Crystal structure of D-amino acid oxidase from Rasamsonia emerson... -

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Basic information

Entry
Database: PDB / ID: 7ct4
TitleCrystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA
ComponentsD-amino acid oxidase
KeywordsFLAVOPROTEIN / Oxidase / D-amino acid
Function / homology
Function and homology information


D-amino acid metabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-amino acid catabolic process / nitrogen utilization / peroxisomal matrix / FAD binding
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / FAD dependent oxidoreductase / FAD dependent oxidoreductase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesTalaromyces emersonii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShimekake, Y. / Hirato, Y. / Okazaki, S. / Funabashi, R. / Goto, M. / Furuichi, T. / Suzuki, H. / Takahashi, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA.
Authors: Shimekake, Y. / Hirato, Y. / Funabashi, R. / Okazaki, S. / Goto, M. / Furuichi, T. / Suzuki, H. / Kera, Y. / Takahashi, S.
History
DepositionAug 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,2028
Polymers170,0604
Non-polymers3,1424
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-74 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.130, 79.130, 366.673
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
D-amino acid oxidase


Mass: 42514.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces emersonii (fungus) / Gene: ReDAO / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A499UB99
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350, Tris-HCl, sodium formate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→68.529 Å / Num. all: 87291 / Num. obs: 87291 / % possible obs: 100 % / Redundancy: 10.1 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Rsym value: 0.094 / Net I/av σ(I): 6 / Net I/σ(I): 13.6 / Num. measured all: 885584
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.11101.0560.7128143127720.371.1751.0562.2100
2.11-2.2410.50.7331.1126097120070.250.8120.7333.3100
2.24-2.3910.10.4611.7114490113460.1610.5120.4615100
2.39-2.5810.10.32.6106618105250.1040.3330.37.4100
2.58-2.8310.60.23.810324997250.0680.220.210.7100
2.83-3.1610.10.126.28867987710.0420.1330.1216.4100
3.16-3.6510.30.0759.37901377050.0260.0840.07526100
3.65-4.479.60.05611.66313965470.0210.0640.05635.4100
4.47-6.329.70.0512.74934450720.0180.0560.0538100
6.32-45.619.50.04213.52681228210.0150.0460.04240.599.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGT

3wgt


Resolution: 2→41.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.1964 / FOM work R set: 0.862 / SU B: 3.26 / SU ML: 0.1 / SU R Cruickshank DPI: 0.0471 / SU Rfree: 0.0385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 4229 4.9 %RANDOM
Rwork0.2063 ---
obs0.2082 82916 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.6 Å2 / Biso mean: 42.243 Å2 / Biso min: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10382 0 212 367 10961
Biso mean--35.18 43.22 -
Num. residues----1376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910876
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.96514884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89351370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14723.914465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.585151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5661569
X-RAY DIFFRACTIONr_chiral_restr0.0890.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218379
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 262 -
Rwork0.21 6193 -
all-6455 -
obs--99.75 %

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