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- PDB-5xxl: Crystal structure of GH3 beta-glucosidase from Bacteroides thetai... -

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Basic information

Entry
Database: PDB / ID: 5xxl
TitleCrystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron
ComponentsPeriplasmic beta-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 3 / beta-glucosidase
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / periplasmic space / metal ion binding
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Periplasmic beta-glucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNakajima, M. / Ishiguro, R. / Tanaka, N. / Abe, K. / Maeda, T. / Miyanaga, A. / Takahash, Y. / Sugimoto, N. / Nakai, H. / Taguchi, H.
CitationJournal: FEBS Lett. / Year: 2017
Title: Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.
Authors: Ishiguro, R. / Tanaka, N. / Abe, K. / Nakajima, M. / Maeda, T. / Miyanaga, A. / Takahashi, Y. / Sugimoto, N. / Nakai, H. / Taguchi, H.
History
DepositionJul 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic beta-glucosidase
B: Periplasmic beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3866
Polymers168,0372
Non-polymers3494
Water22,4651247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-26 kcal/mol
Surface area48790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.940, 167.880, 224.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1520-

HOH

21B-1392-

HOH

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Components

#1: Protein Periplasmic beta-glucosidase


Mass: 84018.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A predicted signal peptide (residues 2-20) is removed when cloning.
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3567 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A1U1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→29.94 Å / Num. obs: 202194 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10
Reflection shellResolution: 1.6→1.69 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U4A

3u4a


Resolution: 1.6→29.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.085 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22738 10325 5.1 %RANDOM
Rwork0.2042 ---
obs0.20538 191817 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.984 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 22 1247 12708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911869
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211316
X-RAY DIFFRACTIONr_angle_refined_deg1.441.96616058
X-RAY DIFFRACTIONr_angle_other_deg0.955326079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93124.294524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25152055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0171578
X-RAY DIFFRACTIONr_chiral_restr0.0830.21769
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022653
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_it0.7371.6885991
X-RAY DIFFRACTIONr_mcbond_other0.7371.6875990
X-RAY DIFFRACTIONr_mcangle_it1.2342.5297515
X-RAY DIFFRACTIONr_mcangle_other1.2342.537516
X-RAY DIFFRACTIONr_scbond_it0.9751.825878
X-RAY DIFFRACTIONr_scbond_other0.9751.8215875
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6352.6758544
X-RAY DIFFRACTIONr_long_range_B_refined3.31413.9214587
X-RAY DIFFRACTIONr_long_range_B_other3.22113.76214329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 715 -
Rwork0.287 14141 -
obs--99.99 %

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