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- PDB-5k6o: Structure of a GH3 b-glucosidase from cow rumen metagenome in com... -

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Basic information

Entry
Database: PDB / ID: 5k6o
TitleStructure of a GH3 b-glucosidase from cow rumen metagenome in complex with galactose
ComponentsB-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA / GALACTOSE
Function / homologyGlycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-galactopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsRamirez-Escudero, M. / Sanz-Aparicio, J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Characterization of a Ruminal beta-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology.
Authors: Ramirez-Escudero, M. / Del Pozo, M.V. / Marin-Navarro, J. / Gonzalez, B. / Golyshin, P.N. / Polaina, J. / Ferrer, M. / Sanz-Aparicio, J.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: B-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,02512
Polymers101,9521
Non-polymers1,07311
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-78 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.924, 119.251, 157.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein B-GLUCOSIDASE


Mass: 101951.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cow rumen / Source: (gene. exp.) metagenome (others) / Gene: glyA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: beta-glucosidase
#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.: 1
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.73 Å3/Da / Density % sol: 54.9 % / Description: Diamond-shaped crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 100mM galactose.
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.1271 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.29→95.08 Å / Num. obs: 44188 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K6L

5k6l


Resolution: 2.29→95.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.988 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22717 2150 4.9 %RANDOM
Rwork0.18134 ---
obs0.18358 41959 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.334 Å2
Baniso -1Baniso -2Baniso -3
1-11.74 Å20 Å20 Å2
2---6.58 Å20 Å2
3----5.16 Å2
Refinement stepCycle: 1 / Resolution: 2.29→95.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6151 0 60 120 6331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196315
X-RAY DIFFRACTIONr_bond_other_d0.0010.025865
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9658535
X-RAY DIFFRACTIONr_angle_other_deg0.947313533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33324.845291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.421151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5921535
X-RAY DIFFRACTIONr_chiral_restr0.0820.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021397
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5834.5333179
X-RAY DIFFRACTIONr_mcbond_other2.584.5323178
X-RAY DIFFRACTIONr_mcangle_it4.0676.7983972
X-RAY DIFFRACTIONr_mcangle_other4.0666.7993973
X-RAY DIFFRACTIONr_scbond_it3.3484.9863136
X-RAY DIFFRACTIONr_scbond_other3.3454.9863136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4167.3034564
X-RAY DIFFRACTIONr_long_range_B_refined7.02435.376763
X-RAY DIFFRACTIONr_long_range_B_other7.02535.3726751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 157 -
Rwork0.323 3040 -
obs--99.97 %

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