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- PDB-5ogz: Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A -

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Basic information

Entry
Database: PDB / ID: 5ogz
TitleCrystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A
ComponentsBeta-glucosidase A
KeywordsSUGAR BINDING PROTEIN / beta/alpha 8 TIM barrel fold cellobiose binding
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSalama-Alber, O. / Bayer, E.
CitationJournal: To Be Published
Title: Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A
Authors: Salama-Alber, O. / Bayer, E.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Beta-glucosidase A
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5556
Polymers105,2052
Non-polymers3504
Water8,629479
1
A: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6982
Polymers52,6021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8564
Polymers52,6021
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.670, 56.220, 94.500
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-glucosidase A / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 52602.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria)
Gene: bglA, Cthe_0212
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P26208, beta-glucosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Lithium sulfate monohydrate, BIS-TRIS, Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.6→93.01 Å / Num. obs: 120756 / % possible obs: 94.61 % / Redundancy: 5 % / Net I/σ(I): 20.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOX

1qox


Resolution: 1.6→93.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.765 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21612 5902 5 %RANDOM
Rwork0.18271 ---
obs0.18438 112516 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20.18 Å2
2---0.06 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.6→93.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 19 479 7814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197609
X-RAY DIFFRACTIONr_bond_other_d0.0020.027081
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.95210304
X-RAY DIFFRACTIONr_angle_other_deg1.119316359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30224.439374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.139151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3871530
X-RAY DIFFRACTIONr_chiral_restr0.1330.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028616
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021810
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_it1.8261.7593630
X-RAY DIFFRACTIONr_mcbond_other1.8261.7583629
X-RAY DIFFRACTIONr_mcangle_it2.5472.6374548
X-RAY DIFFRACTIONr_mcangle_other2.5472.6374549
X-RAY DIFFRACTIONr_scbond_it2.6482.023979
X-RAY DIFFRACTIONr_scbond_other2.6482.023979
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9632.915757
X-RAY DIFFRACTIONr_long_range_B_refined5.37414.6439223
X-RAY DIFFRACTIONr_long_range_B_other5.37414.6449224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 430 -
Rwork0.221 8217 -
obs--93.9 %

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