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

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Basic information

Entry
Database: PDB / ID: 7byv
TitleCrystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208Q 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, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
beta-D-galactopyranose / Galactan 1,3-beta-galactosidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,4167
Polymers45,6631
Non-polymers1,7546
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Software (PISA) determined protein interfaces has not revealed any specific interactions that could result in the formation of stable quaternary structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint13 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.080, 50.412, 75.698
Angle α, β, γ (deg.)90.000, 111.328, 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

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Protein , 1 types, 1 molecules A

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


Mass: 45662.793 Da / Num. of mol.: 1 / Mutation: E208Q
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 , 4 types, 5 molecules

#2: 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
#3: Polysaccharide beta-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: isolated from a natural 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: 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.: 2 / 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
#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 228 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.5 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16 % (w/v) polyethylene glycol (PEG) 10000, 95 mM ammonium sulfate, 95 mM bis-tris, 4.8 % 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: Oct 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 16007 / % possible obs: 96.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 29.91 Å2 / Rsym value: 0.143 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 702 / Rsym value: 0.339 / % possible all: 83

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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: 2.5→29.79 Å / SU ML: 0.3477 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 799 5.07 %
Rwork0.1662 14960 -
obs0.1701 15759 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.48 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 114 227 3568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823434
X-RAY DIFFRACTIONf_angle_d0.93124690
X-RAY DIFFRACTIONf_chiral_restr0.0579525
X-RAY DIFFRACTIONf_plane_restr0.0052605
X-RAY DIFFRACTIONf_dihedral_angle_d5.00072640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.36921270.25092252X-RAY DIFFRACTION88.37
2.66-2.860.31361370.23042496X-RAY DIFFRACTION97.41
2.86-3.150.28731360.20872561X-RAY DIFFRACTION99.19
3.15-3.60.24011390.16262497X-RAY DIFFRACTION97.96
3.6-4.540.22591150.12822531X-RAY DIFFRACTION96.96
4.54-29.790.17391450.13332623X-RAY DIFFRACTION98.96

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