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- PDB-5ta9: Crystal structure of BuGH117Bwt in complex with neoagarobiose -

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Basic information

Entry
Database: PDB / ID: 5ta9
TitleCrystal structure of BuGH117Bwt in complex with neoagarobiose
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / agarase / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
3,6-anhydro-alpha-L-galactopyranose / beta-D-galactopyranose / 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)184,01416
Polymers182,5484
Non-polymers1,46612
Water8,053447
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0044
Polymers45,6371
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Glycoside Hydrolase
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0078
Polymers91,2742
Non-polymers7336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-32 kcal/mol
Surface area27110 Å2
MethodPISA
6
C: Glycoside Hydrolase
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0078
Polymers91,2742
Non-polymers7336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-30 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.511, 104.380, 198.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycoside Hydrolase


Mass: 45636.973 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: A0A2D0TCD6*PLUS
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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
#3: Sugar
ChemComp-AAL / 3,6-anhydro-alpha-L-galactopyranose / 3,6-ANHYDRO-L-GALACTOSE / 3,6-anhydro-alpha-L-galactose / 3,6-anhydro-galactose


Type: L-saccharide, alpha linking / Mass: 162.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1-0.18M LiSo4, 0.1M Tris-HCl, 25-30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→99.25 Å / Num. obs: 65697 / % possible obs: 96 % / Redundancy: 8.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.825 / % possible all: 90

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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 / Resolution: 2.4→99.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.431 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.279
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 3303 5 %RANDOM
Rwork0.2071 ---
obs0.2095 62315 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.2 Å2 / Biso mean: 41.588 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---2 Å20 Å2
3---2.32 Å2
Refinement stepCycle: final / Resolution: 2.4→99.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11798 0 96 447 12341
Biso mean--45.37 32.04 -
Num. residues----1476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212247
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210915
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93716640
X-RAY DIFFRACTIONr_angle_other_deg0.892325247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0951472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55924.148581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95151933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8361560
X-RAY DIFFRACTIONr_chiral_restr0.0750.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022854
X-RAY DIFFRACTIONr_mcbond_it1.724.2095900
X-RAY DIFFRACTIONr_mcbond_other1.7194.2095899
X-RAY DIFFRACTIONr_mcangle_it2.8376.3077368
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 252 -
Rwork0.284 4219 -
all-4471 -
obs--89.15 %

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