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- PDB-7byx: Crystal structure of exo-beta-1,3-galactanase from Phanerochaete ... -

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Basic information

Entry
Database: PDB / ID: 7byx
TitleCrystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208A with beta-1,3-galactotriose
ComponentsGalactan 1,3-beta-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase family 43 / exo-beta-1 / 3-galactanase / arabinogalactan degrade / complex with beta-1 / 3-galactotriose / carbohydrate binding module family 35
Function / homology
Function and homology information


galactan 1,3-beta-galactosidase / galactan 1,3-beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Galactan 1,3-beta-galactosidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsuyama, K. / Ishida, T. / Kishine, N. / Fujimoto, Z. / Igarashi, K. / Kaneko, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05494 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium .
Authors: Matsuyama, K. / Kishine, N. / Fujimoto, Z. / Sunagawa, N. / Kotake, T. / Tsumuraya, Y. / Samejima, M. / Igarashi, K. / Kaneko, S.
History
DepositionApr 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 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 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_special_symmetry.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactan 1,3-beta-galactosidase
B: Galactan 1,3-beta-galactosidase
C: Galactan 1,3-beta-galactosidase
D: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,23252
Polymers181,9104
Non-polymers10,32248
Water18,1231006
1
A: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,72917
Polymers45,4781
Non-polymers3,25116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,76010
Polymers45,4781
Non-polymers2,2829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,94412
Polymers45,4781
Non-polymers2,46611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,80013
Polymers45,4781
Non-polymers2,32212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.737, 156.737, 147.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
D: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-935-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Galactan 1,3-beta-galactosidase / exo-beta-1 / 3-galactanase


Mass: 45477.613 Da / Num. of mol.: 4 / Mutation: E208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: Pc1,3Gal43A / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: Q50KB2, galactan 1,3-beta-galactosidase

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Sugars , 6 types, 16 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-Galp]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#10: 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.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
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

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Non-polymers , 4 types, 1038 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.06 % / Description: bipyramidial
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M potassium nitrate, 15 % (w/v) polyethylene glycol 6000, 20 mM sodium citrate, 5 % glycerol, 10 mM beta-1,3-galactotriose

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 92497 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.167 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8510 / Rsym value: 0.627 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
REFMAC5.8.0158refinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BYS

7bys


Resolution: 2.3→31.14 Å / SU ML: 0.2633 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 4569 4.97 %Random selection
Rwork0.161 87425 --
obs0.1637 91994 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 678 1006 14540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007613873
X-RAY DIFFRACTIONf_angle_d0.951518897
X-RAY DIFFRACTIONf_chiral_restr0.06322116
X-RAY DIFFRACTIONf_plane_restr0.00532416
X-RAY DIFFRACTIONf_dihedral_angle_d4.37619641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31361330.23332531X-RAY DIFFRACTION87
2.33-2.350.28061720.2222664X-RAY DIFFRACTION91.99
2.35-2.380.25691360.2182871X-RAY DIFFRACTION97.47
2.38-2.410.27051620.21332871X-RAY DIFFRACTION99.09
2.41-2.440.32821650.2112909X-RAY DIFFRACTION99.19
2.44-2.480.26741540.20792904X-RAY DIFFRACTION99.41
2.48-2.510.28961560.19962895X-RAY DIFFRACTION99.16
2.51-2.550.27891410.20082892X-RAY DIFFRACTION99.21
2.55-2.590.30261360.19992911X-RAY DIFFRACTION99.19
2.59-2.630.23811690.18742874X-RAY DIFFRACTION99.19
2.63-2.680.26321600.18312917X-RAY DIFFRACTION99.64
2.68-2.730.24881540.18512913X-RAY DIFFRACTION99.22
2.73-2.780.26591370.18872902X-RAY DIFFRACTION99.31
2.78-2.840.2441120.18392990X-RAY DIFFRACTION99.52
2.84-2.90.2261520.18172896X-RAY DIFFRACTION99.25
2.9-2.960.25051560.16882881X-RAY DIFFRACTION99.15
2.96-3.040.22691390.17152969X-RAY DIFFRACTION99.65
3.04-3.120.22231830.16052923X-RAY DIFFRACTION99.74
3.12-3.210.19491450.15462925X-RAY DIFFRACTION99.55
3.21-3.320.21571750.15812911X-RAY DIFFRACTION99.87
3.32-3.430.23571300.15492978X-RAY DIFFRACTION99.94
3.43-3.570.1981450.14292944X-RAY DIFFRACTION99.9
3.57-3.730.17971790.13842921X-RAY DIFFRACTION99.97
3.73-3.930.18751370.1392981X-RAY DIFFRACTION99.97
3.93-4.180.19911610.1362967X-RAY DIFFRACTION100
4.18-4.50.15151290.12322991X-RAY DIFFRACTION99.94
4.5-4.950.1461840.11492949X-RAY DIFFRACTION99.9
4.95-5.660.18111500.13483003X-RAY DIFFRACTION99.9
5.66-7.120.21440.1613038X-RAY DIFFRACTION100
7.12-31.140.20471730.18523104X-RAY DIFFRACTION99.45

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