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- PDB-8yfh: Structure of alpha-1,3-glucanase agn1 -

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Basic information

Entry
Database: PDB / ID: 8yfh
TitleStructure of alpha-1,3-glucanase agn1
ComponentsGlucan endo-1,3-alpha-glucosidase agn1
KeywordsHYDROLASE / glucanase
Function / homology
Function and homology information


cell septum edging catabolic process / glucan endo-1,3-alpha-glucosidase / glucan endo-1,3-alpha-glucosidase activity / fungal-type cell wall disassembly involved in conjugation with cellular fusion / mating projection actin fusion focus / mating projection tip / extracellular region
Similarity search - Function
Glycoside hydrolase family 71 / Glycosyl hydrolase family 71
Similarity search - Domain/homology
Glucan endo-1,3-alpha-glucosidase agn1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe DM3650 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoraguch, Y. / Yano, S. / Makabe, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of alpha-1,3-glucanase agn1
Authors: Horaguchi, Y. / Yano, S. / Makabe, K.
History
DepositionFeb 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucan endo-1,3-alpha-glucosidase agn1
B: Glucan endo-1,3-alpha-glucosidase agn1
C: Glucan endo-1,3-alpha-glucosidase agn1


Theoretical massNumber of molelcules
Total (without water)133,6053
Polymers133,6053
Non-polymers00
Water20,9331162
1
A: Glucan endo-1,3-alpha-glucosidase agn1


Theoretical massNumber of molelcules
Total (without water)44,5351
Polymers44,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucan endo-1,3-alpha-glucosidase agn1


Theoretical massNumber of molelcules
Total (without water)44,5351
Polymers44,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucan endo-1,3-alpha-glucosidase agn1


Theoretical massNumber of molelcules
Total (without water)44,5351
Polymers44,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.534, 114.514, 109.111
Angle α, β, γ (deg.)90.000, 104.236, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glucan endo-1,3-alpha-glucosidase agn1 / Endo-1 / 3-alpha-glucanase agn1


Mass: 44534.848 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe DM3650 (yeast)
Gene: agn1, SPAC14C4.09 / Production host: Escherichia coli (E. coli)
References: UniProt: O13716, glucan endo-1,3-alpha-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.9M Disodium Malonate, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 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: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→48.01 Å / Num. obs: 158150 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.34 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.3
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 7813 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.99 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 7578 4.96 %
Rwork0.1654 145243 -
obs0.1667 152821 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9459 0 0 1162 10621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619753
X-RAY DIFFRACTIONf_angle_d0.776213353
X-RAY DIFFRACTIONf_chiral_restr0.0541419
X-RAY DIFFRACTIONf_plane_restr0.00591725
X-RAY DIFFRACTIONf_dihedral_angle_d5.97741311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.26382360.22974852X-RAY DIFFRACTION99.96
1.82-1.840.25782510.22364852X-RAY DIFFRACTION100
1.84-1.860.26982490.21014792X-RAY DIFFRACTION99.94
1.86-1.890.22962270.20624855X-RAY DIFFRACTION99.98
1.89-1.910.25682570.20214837X-RAY DIFFRACTION99.98
1.91-1.940.24432570.19974822X-RAY DIFFRACTION99.96
1.94-1.970.21362560.18814795X-RAY DIFFRACTION99.94
1.97-20.21982610.18094816X-RAY DIFFRACTION99.9
2-2.030.21622690.17914841X-RAY DIFFRACTION99.98
2.03-2.060.20832670.17954822X-RAY DIFFRACTION99.94
2.06-2.10.20332560.17374820X-RAY DIFFRACTION99.98
2.1-2.130.212470.17484809X-RAY DIFFRACTION99.98
2.13-2.170.21072330.16924854X-RAY DIFFRACTION99.94
2.17-2.220.20922490.16624792X-RAY DIFFRACTION99.9
2.22-2.270.19632560.17244866X-RAY DIFFRACTION99.98
2.27-2.320.2052530.16834843X-RAY DIFFRACTION100
2.32-2.380.19332430.17574834X-RAY DIFFRACTION100
2.38-2.440.21672380.16834852X-RAY DIFFRACTION99.86
2.44-2.510.20832550.17614806X-RAY DIFFRACTION99.94
2.51-2.590.21342390.17434896X-RAY DIFFRACTION100
2.59-2.690.20632550.17794809X-RAY DIFFRACTION99.94
2.69-2.790.20372420.18274879X-RAY DIFFRACTION99.94
2.79-2.920.21082390.18344854X-RAY DIFFRACTION100
2.92-3.070.22582580.17974822X-RAY DIFFRACTION100
3.08-3.270.18712780.17184842X-RAY DIFFRACTION99.98
3.27-3.520.18422980.16034822X-RAY DIFFRACTION99.96
3.52-3.870.19152600.14464855X-RAY DIFFRACTION99.98
3.87-4.420.14722340.12714865X-RAY DIFFRACTION99.94
4.42-5.550.12852390.13284910X-RAY DIFFRACTION99.92
5.55-19.990.15792760.16344929X-RAY DIFFRACTION99.83

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