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- PDB-5t9a: Crystal structure of BuGH2Cwt -

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Basic information

Entry
Database: PDB / ID: 5t9a
TitleCrystal structure of BuGH2Cwt
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / 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
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPluvinage, B. / Boraston, A.B. / Abbott, W.D.
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)388,10913
Polymers387,4834
Non-polymers6279
Water13,601755
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1195
Polymers96,8711
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9672
Polymers96,8711
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0293
Polymers96,8711
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9953
Polymers96,8711
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.140, 121.350, 124.520
Angle α, β, γ (deg.)70.900, 87.470, 78.960
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium sulfate, 0.1 M Tris-HCl, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→117.64 Å / Num. obs: 137926 / % possible obs: 97.8 % / Redundancy: 2.2 % / CC1/2: 0.935 / Rmerge(I) obs: 0.121 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.548 / CC1/2: 0.298 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CU6

4cu6


Resolution: 2.5→117.64 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.864 / SU B: 12.359 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.33
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 6086 4.9 %RANDOM
Rwork0.2083 ---
obs0.2108 117397 87.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.36 Å2 / Biso mean: 30.07 Å2 / Biso min: 4.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.02 Å20.02 Å2
2---0.01 Å20.02 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.5→117.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25963 0 38 755 26756
Biso mean--45.21 22.91 -
Num. residues----3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01926690
X-RAY DIFFRACTIONr_bond_other_d0.0020.0224154
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.92536222
X-RAY DIFFRACTIONr_angle_other_deg0.884355490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43753241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82124.11305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.625154297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.94315141
X-RAY DIFFRACTIONr_chiral_restr0.0720.23797
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026567
X-RAY DIFFRACTIONr_mcbond_it1.0133.07312982
X-RAY DIFFRACTIONr_mcbond_other1.0133.07312981
X-RAY DIFFRACTIONr_mcangle_it1.7764.60716217
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 260 -
Rwork0.301 5023 -
all-5283 -
obs--50.92 %

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