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- PDB-7jwf: Crystal structure of PdGH110B D344N in complex with alpha-(1,3)-g... -

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Basic information

Entry
Database: PDB / ID: 7jwf
TitleCrystal structure of PdGH110B D344N in complex with alpha-(1,3)-galactobiose
ComponentsGlycoside hydrolase family 110
KeywordsHYDROLASE / beta helix
Function / homologyACETATE ION / IODIDE ION / MALONIC ACID / MALONATE ION / D-MALATE
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.187 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 25, 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 1.3Oct 18, 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: Glycoside hydrolase family 110
B: Glycoside hydrolase family 110
C: Glycoside hydrolase family 110
D: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,898200
Polymers279,3834
Non-polymers21,515196
Water29,9231661
1
A: Glycoside hydrolase family 110
B: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,339102
Polymers139,6912
Non-polymers10,647100
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glycoside hydrolase family 110
hetero molecules

C: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,55998
Polymers139,6912
Non-polymers10,86896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Unit cell
Length a, b, c (Å)98.517, 124.763, 142.423
Angle α, β, γ (deg.)90.000, 93.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glycoside hydrolase family 110


Mass: 69845.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 11 types, 1853 molecules

#3: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 119 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#11: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#12: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1661 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, HEPES, NaI, Tacsimate

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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: 2.187→30 Å / Num. obs: 174470 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.991 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 7427 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JW4

7jw4


Resolution: 2.187→29.759 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 8677 5.04 %
Rwork0.2049 163631 -
obs0.2065 172308 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.47 Å2 / Biso mean: 34.902 Å2 / Biso min: 18.51 Å2
Refinement stepCycle: final / Resolution: 2.187→29.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18427 0 526 1661 20614
Biso mean--44.79 38.52 -
Num. residues----2330
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1874-2.21230.32242150.2703422576
2.2123-2.23830.30452550.2808561799
2.2383-2.26560.34352840.294548499
2.2656-2.29420.28513080.2435551699
2.2942-2.32440.36022820.2907546599
2.3244-2.35630.30782980.2604557899
2.3563-2.38990.32432930.2463549699
2.3899-2.42560.30662890.2478557399
2.4256-2.46340.2852970.2401558999
2.4634-2.50380.2442970.2345552299
2.5038-2.5470.27123180.2352551099
2.547-2.59320.32513160.2427553299
2.5932-2.64310.30842790.241547599
2.6431-2.6970.29052850.2405551399
2.697-2.75560.28942950.2359543598
2.7556-2.81970.27262830.2485544297
2.8197-2.89010.31582670.2465539896
2.8901-2.96820.27772750.242532196
2.9682-3.05550.2742850.2343541896
3.0555-3.1540.24393140.2241540097
3.154-3.26660.24132850.2098553898
3.2666-3.39720.23092820.2002555499
3.3972-3.55160.2132900.184553799
3.5516-3.73850.19573230.16975585100
3.7385-3.97220.20393260.1734545498
3.9722-4.27810.23010.1699526094
4.2781-4.70710.15982670.1491549797
4.7071-5.38470.18592760.1558551198
5.3847-6.77090.21573100.1922558699
6.7709-29.7590.20512820.1995560097

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