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- PDB-9kp8: Crystal structure of FAD-dependent oxidase CpaO -

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Basic information

Entry
Database: PDB / ID: 9kp8
TitleCrystal structure of FAD-dependent oxidase CpaO
Componentsalpha-glucosidase,Beta-cyclopiazonate dehydrogenase
KeywordsOXIDOREDUCTASE / oxidase / FAD-dependent
Function / homology
Function and homology information


beta-cyclopiazonate dehydrogenase / beta-cyclopiazonate dehydrogenase activity / mating / alpha-1,4-glucosidase activity / alpha-glucosidase / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Mating factor alpha precursor, N-terminal / Mating factor alpha precursor N-terminus / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain ...Mating factor alpha precursor, N-terminal / Mating factor alpha precursor N-terminus / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Amine oxidase / Flavin containing amine oxidoreductase / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / FAD/NAD(P)-binding domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alpha-glucosidase / Beta-cyclopiazonate dehydrogenase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsChang, C.Y. / Kuo, Y.M. / Cheng, T. / Liang, C.H. / Hsiao, P.Y. / Lin, Y.C. / Wang, N.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of FAD-dependent oxidase CpaO
Authors: Chang, C.Y. / Kuo, Y.M. / Cheng, T. / Liang, C.H. / Hsiao, P.Y. / Lin, Y.C. / Wang, N.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-glucosidase,Beta-cyclopiazonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8829
Polymers60,0481
Non-polymers1,8338
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.245, 118.245, 68.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein alpha-glucosidase,Beta-cyclopiazonate dehydrogenase / Maltase / Beta-Cyclopiazonate oxidocyclase / FAD-dependent oxidoreductase cpaO


Mass: 60048.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: AAG, cpaO, AO090026000003 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0AA49QBA5, UniProt: Q2UG11, alpha-glucosidase, beta-cyclopiazonate dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.179→30 Å / Num. obs: 178136 / % possible obs: 98.96 % / Redundancy: 9 % / Rrim(I) all: 0.038 / Net I/σ(I): 58.19
Reflection shellResolution: 1.179→1.22 Å / Mean I/σ(I) obs: 5.33 / Num. unique obs: 169210 / CC1/2: 0.941 / Rpim(I) all: 0.148 / Rrim(I) all: 0.431

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data collection
SCALAdata scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.179→24.246 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: NONE / ESU R: 0.033 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1736 8926 5.011 %
Rwork0.1635 169210 -
all0.164 --
obs-178136 98.959 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20 Å2
2--0.001 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.179→24.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 115 697 4246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163283
X-RAY DIFFRACTIONr_angle_refined_deg1.0171.6575051
X-RAY DIFFRACTIONr_angle_other_deg0.6021.5697565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.949521
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.21951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78110549
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.72610182
X-RAY DIFFRACTIONr_chiral_restr0.050.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024325
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02866
X-RAY DIFFRACTIONr_nbd_refined0.2640.2772
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2480.23158
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21828
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2462
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.310.226
X-RAY DIFFRACTIONr_nbd_other0.2470.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.283
X-RAY DIFFRACTIONr_mcbond_it0.5951.4961748
X-RAY DIFFRACTIONr_mcbond_other0.5941.4961748
X-RAY DIFFRACTIONr_mcangle_it0.9532.6912192
X-RAY DIFFRACTIONr_mcangle_other0.9532.6922193
X-RAY DIFFRACTIONr_scbond_it1.0361.6661942
X-RAY DIFFRACTIONr_scbond_other1.0371.6491931
X-RAY DIFFRACTIONr_scangle_it1.6572.9922859
X-RAY DIFFRACTIONr_scangle_other1.662.9622842
X-RAY DIFFRACTIONr_lrange_it5.59323.3954722
X-RAY DIFFRACTIONr_lrange_other5.16118.2564458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.179-1.2090.2136830.20912217X-RAY DIFFRACTION97.3071
1.209-1.2420.216290.212080X-RAY DIFFRACTION98.6035
1.242-1.2780.196780.1911722X-RAY DIFFRACTION98.734
1.278-1.3180.2046170.18611451X-RAY DIFFRACTION99.1456
1.318-1.3610.1835850.1811173X-RAY DIFFRACTION99.1985
1.361-1.4080.2015790.17610809X-RAY DIFFRACTION99.2591
1.408-1.4610.1885640.1710423X-RAY DIFFRACTION99.6463
1.461-1.5210.1795430.16810044X-RAY DIFFRACTION99.633
1.521-1.5880.1694760.169700X-RAY DIFFRACTION99.7451
1.588-1.6650.1714760.1619284X-RAY DIFFRACTION99.8465
1.665-1.7550.1714090.1638844X-RAY DIFFRACTION99.9244
1.755-1.8610.1724960.1618288X-RAY DIFFRACTION99.9545
1.861-1.9880.174080.1557869X-RAY DIFFRACTION99.9879
1.988-2.1460.1623900.157322X-RAY DIFFRACTION99.9741
2.146-2.3490.1733180.1516783X-RAY DIFFRACTION99.9859
2.349-2.6240.1743140.1556145X-RAY DIFFRACTION99.9845
2.624-3.0240.1692860.1615411X-RAY DIFFRACTION99.8773
3.024-3.6890.1632250.1584535X-RAY DIFFRACTION98.3471
3.689-5.1580.1521610.1523286X-RAY DIFFRACTION90.9259
5.158-100.216890.2161824X-RAY DIFFRACTION86.3267

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