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- PDB-5k6l: Structure of a GH3 b-glucosidase from cow rumen metagenome -

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Basic information

Entry
Database: PDB / ID: 5k6l
TitleStructure of a GH3 b-glucosidase from cow rumen metagenome
ComponentsB-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA
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
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 1.3Jan 10, 2024Group: 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: B-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,78110
Polymers101,9521
Non-polymers8299
Water12,142674
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-2 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.215, 119.724, 157.489
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): Rosetta 2 / References: beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.76 Å3/Da / Density % sol: 55.54 % / Description: Elongated bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.1M Na malonate pH 7.0, then soaked in 25% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.83→95.31 Å / Num. obs: 84644 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.7
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.1 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x42

2x42


Resolution: 1.83→95.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.318 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17854 4317 5.1 %RANDOM
Rwork0.15676 ---
obs0.15789 80259 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.032 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.83→95.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 54 674 6870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196310
X-RAY DIFFRACTIONr_bond_other_d0.0010.025901
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9628513
X-RAY DIFFRACTIONr_angle_other_deg0.891313615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97224.845291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.126151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6891535
X-RAY DIFFRACTIONr_chiral_restr0.0740.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021400
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_it0.8431.8613180
X-RAY DIFFRACTIONr_mcbond_other0.8391.8593179
X-RAY DIFFRACTIONr_mcangle_it1.4262.7863975
X-RAY DIFFRACTIONr_mcangle_other1.4262.7873976
X-RAY DIFFRACTIONr_scbond_it1.1862.0553130
X-RAY DIFFRACTIONr_scbond_other1.1852.0553130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9533.0074539
X-RAY DIFFRACTIONr_long_range_B_refined4.30515.9227602
X-RAY DIFFRACTIONr_long_range_B_other3.89215.3657261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.835→1.883 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 294 -
Rwork0.219 5334 -
obs--90.48 %

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