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

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Basic information

Entry
Database: PDB / ID: 7bys
TitleCrystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form
ComponentsGalactan 1,3-beta-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase family 43 / exo-beta-1 / 3-galactanase / arabinogalactan degrade / apo form / 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
CITRIC ACID / Galactan 1,3-beta-galactosidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 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 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,78610
Polymers91,0712
Non-polymers1,7158
Water22,3751242
1
A: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2105
Polymers45,5361
Non-polymers6754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint6 kcal/mol
Surface area16000 Å2
MethodPISA
2
B: Galactan 1,3-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5765
Polymers45,5361
Non-polymers1,0404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint10 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.470, 66.262, 74.021
Angle α, β, γ (deg.)72.030, 84.680, 82.150
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 45535.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Plasmid: pPICZaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: Q50KB2, galactan 1,3-beta-galactosidase

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Sugars , 2 types, 4 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: 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: 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 , 3 types, 1246 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1242 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.0540.03
22.4750.1plate
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop5.52.1 M ammonium sulfate, 0.1 M citrate buffer pH 5.5.
2932vapor diffusion5.516% (w/v) polyethylene glycol (PEG) 10000 95 mM ammonium sulfate 95 mM bis-tris 4.8% (v/v) glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1951N
2952N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.90646
SYNCHROTRONPhoton Factory BL-6A20.97882,0.97950,0.98300,0.96400
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 11, 2008
ADSC QUANTUM 4r2CCDNov 26, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.906461
20.978821
30.97951
40.9831
50.9641
ReflectionResolution: 1.4→50 Å / Num. obs: 136692 / % possible obs: 95.6 % / Redundancy: 1.9 % / Rsym value: 0.054 / Net I/σ(I): 22.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12747 / Rsym value: 0.37 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.16_356refinement
REFMAC5.8.0238refinement
Cootmodel building
MOLREPphasing
ARP/wARPmodel building
SOLVEphasing
RESOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→8 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 6862 -Random selection
Rwork0.1547 ---
obs0.1562 136655 95.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.21 Å2 / Biso mean: 17.1719 Å2 / Biso min: 5.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 109 1242 7787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.410.27831830.23213641X-RAY DIFFRACTION81.59
1.41-1.430.27162230.22594031X-RAY DIFFRACTION89.33
1.43-1.450.24262240.21854195X-RAY DIFFRACTION92.43
1.45-1.470.23751820.2134196X-RAY DIFFRACTION93.85
1.47-1.490.2342160.20864229X-RAY DIFFRACTION94.65
1.49-1.510.24532210.1974309X-RAY DIFFRACTION95.23
1.51-1.530.23162340.19594263X-RAY DIFFRACTION95.5
1.53-1.550.21982330.18794387X-RAY DIFFRACTION95.71
1.55-1.570.21362200.1894283X-RAY DIFFRACTION95.61
1.57-1.60.21942260.18144297X-RAY DIFFRACTION95.93
1.6-1.630.22212420.18074374X-RAY DIFFRACTION96.01
1.63-1.660.22752210.17344329X-RAY DIFFRACTION96.17
1.66-1.690.19982500.1754385X-RAY DIFFRACTION96.28
1.69-1.720.23442470.17354274X-RAY DIFFRACTION96.29
1.72-1.760.18852090.1694413X-RAY DIFFRACTION96.8
1.76-1.80.18772300.17114312X-RAY DIFFRACTION96.64
1.8-1.840.19792500.17054386X-RAY DIFFRACTION96.91
1.84-1.890.18672340.17384338X-RAY DIFFRACTION96.86
1.89-1.950.18882180.16334413X-RAY DIFFRACTION97.15
1.95-2.010.19191900.15874398X-RAY DIFFRACTION97.39
2.01-2.080.16522310.1514406X-RAY DIFFRACTION97.52
2.08-2.160.17942200.15114414X-RAY DIFFRACTION97.76
2.16-2.260.19612240.15174452X-RAY DIFFRACTION97.93
2.26-2.370.18162650.15554409X-RAY DIFFRACTION98.03
2.37-2.520.1862440.15644398X-RAY DIFFRACTION98.14
2.52-2.710.18032470.15494430X-RAY DIFFRACTION98.5
2.71-2.960.21582610.15314397X-RAY DIFFRACTION98.75
2.96-3.370.17452400.13524494X-RAY DIFFRACTION98.91
3.37-4.140.13682530.11814419X-RAY DIFFRACTION98.98
4.14-80.14682240.12074444X-RAY DIFFRACTION98.23

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