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- PDB-5t9g: Crystal structure of BuGH2Cwt in complex with Galactoisofagomine -

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Basic information

Entry
Database: PDB / ID: 5t9g
TitleCrystal structure of BuGH2Cwt in complex with Galactoisofagomine
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-galacto-isofagomine / Glycoside Hydrolase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPluvinage, B. / Boraston, A.B.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont.
Authors: Pluvinage, B. / Grondin, J.M. / Amundsen, C. / Klassen, L. / Moote, P.E. / Xiao, Y. / Thomas, D. / Pudlo, N.A. / Anele, A. / Martens, E.C. / Inglis, G.D. / Uwiera, R.E.R. / Boraston, A.B. / Abbott, D.W.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
B: Glycoside Hydrolase
C: Glycoside Hydrolase
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,94022
Polymers387,4834
Non-polymers1,45818
Water15,331851
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2045
Polymers96,8711
Non-polymers3334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3287
Polymers96,8711
Non-polymers4586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3287
Polymers96,8711
Non-polymers4586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0803
Polymers96,8711
Non-polymers2092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.230, 121.130, 124.459
Angle α, β, γ (deg.)70.630, 86.800, 78.770
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glycoside Hydrolase


Mass: 96870.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: NP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCC9*PLUS
#2: Chemical
ChemComp-GIF / D-galacto-isofagomine


Mass: 147.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium citrate, 20-24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.4→117.41 Å / Num. obs: 139311 / % possible obs: 87.6 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2 / CC1/2: 0.786 / % possible all: 82.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T9A

5t9a


Resolution: 2.4→117.41 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.834 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.298
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 6968 5 %RANDOM
Rwork0.2067 ---
obs0.2093 132324 87.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.15 Å2 / Biso mean: 30.647 Å2 / Biso min: 3.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å2-0.91 Å22.16 Å2
2---3.63 Å20.86 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.4→117.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26014 0 96 851 26961
Biso mean--35.26 22.24 -
Num. residues----3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01926913
X-RAY DIFFRACTIONr_bond_other_d0.0020.0224329
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.92736520
X-RAY DIFFRACTIONr_angle_other_deg0.904355942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6853260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65524.1851338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.697154343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.38715145
X-RAY DIFFRACTIONr_chiral_restr0.0760.23818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026614
X-RAY DIFFRACTIONr_mcbond_it1.093.1213029
X-RAY DIFFRACTIONr_mcbond_other1.093.1213024
X-RAY DIFFRACTIONr_mcangle_it1.8354.67716290
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 451 -
Rwork0.324 9133 -
all-9584 -
obs--81.94 %

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