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- PDB-7jw4: Crystal structure of PdGH110B in complex with D-galactose -

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Basic information

Entry
Database: PDB / ID: 7jw4
TitleCrystal structure of PdGH110B in complex with D-galactose
ComponentsGlycoside hydrolase family 110
KeywordsHYDROLASE / beta helix
Function / homologybeta-D-galactopyranose / alpha-D-galactopyranose / NICKEL (II) ION
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.342 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens.
Authors: McGuire, B.E. / Hettle, A.G. / Vickers, C. / King, D.T. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 6, 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.name
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 110
B: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4229
Polymers139,6932
Non-polymers7297
Water16,232901
1
A: Glycoside hydrolase family 110
hetero molecules

A: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,60210
Polymers139,6932
Non-polymers9098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6670 Å2
ΔGint-51 kcal/mol
Surface area40850 Å2
MethodPISA
2
B: Glycoside hydrolase family 110
hetero molecules

B: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,2428
Polymers139,6932
Non-polymers5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area5790 Å2
ΔGint-18 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.786, 128.093, 100.014
Angle α, β, γ (deg.)90.000, 123.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 110


Mass: 69846.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
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 , 3 types, 905 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 6000, HEPES, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.342→30 Å / Num. obs: 74084 / % possible obs: 99.6 % / Redundancy: 4 % / CC1/2: 0.989 / Net I/σ(I): 10.4
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 4528 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wildtype PdGH110B

Resolution: 2.342→24.982 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 3684 4.97 %
Rwork0.1848 70400 -
obs0.187 74084 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.82 Å2 / Biso mean: 34.8971 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2.342→24.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 0 40 901 10228
Biso mean--35.72 40.66 -
Num. residues----1182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.342-2.37260.34251260.2621249190
2.3726-2.40510.28291340.222270999
2.4051-2.43940.23331320.2175275099
2.4394-2.47580.30141550.2232702100
2.4758-2.51440.26731640.21722712100
2.5144-2.55560.29571470.20282733100
2.5556-2.59970.28471400.20772723100
2.5997-2.64690.26291350.19882746100
2.6469-2.69770.25641250.19122765100
2.6977-2.75270.26091350.20242715100
2.7527-2.81250.27481320.20282790100
2.8125-2.87780.27161490.21042724100
2.8778-2.94970.29541690.19142712100
2.9497-3.02930.24751600.18662708100
3.0293-3.11830.24911580.19332734100
3.1183-3.21870.24121300.2011272299
3.2187-3.33350.25611510.1922271099
3.3335-3.46670.29061690.2437256895
3.4667-3.6240.2471210.1926270798
3.624-3.81440.22891240.20082771100
3.8144-4.05250.23361180.1923263195
4.0525-4.36380.2011470.1568258695
4.3638-4.80020.14931480.1171270898
4.8002-5.48840.16771410.1361272799
5.4884-6.89060.17651240.17142771100
6.8906-24.9820.17351500.165278599

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