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- PDB-5m6g: Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolysp... -

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Basic information

Entry
Database: PDB / ID: 5m6g
TitleCrystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea
ComponentsBeta-glucosidase
KeywordsHYDROLASE / 2-DOMAIN FOLD
Function / homology
Function and homology information


glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
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 / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / sorbitol / Beta-glucosidase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea D (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.829 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
CitationJournal: To Be Published
Title: Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea
Authors: Gabdulkhakov, A. / Tishchenko, S.
History
DepositionOct 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / reflns_shell / struct_ref / struct_ref_seq
Item: _entity.pdbx_ec / _entity_src_gen.gene_src_strain ..._entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 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: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,13412
Polymers65,3801
Non-polymers75411
Water5,008278
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-44 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.292, 75.717, 113.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-glucosidase / / Glucan 1 / 4-beta-glucosidase


Mass: 65379.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea D (bacteria)
Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338
Gene: celD, SACE_6502, A8924_6851 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A4FNP6, glucan 1,4-beta-glucosidase
#5: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol / Sorbitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6

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Non-polymers , 4 types, 288 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20K, 100mM MES Sodium Salt, 80 mM Mangan II Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033121 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033121 Å / Relative weight: 1
ReflectionResolution: 1.829→50 Å / Num. obs: 47457 / % possible obs: 95.1 % / Redundancy: 3.35 % / Net I/σ(I): 11.27

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ieq

1ieq


Resolution: 1.829→45.511 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.86
RfactorNum. reflection% reflection
Rfree0.2035 2099 4.42 %
Rwork0.1716 --
obs0.173 47437 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.829→45.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 46 278 4675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064503
X-RAY DIFFRACTIONf_angle_d0.8196113
X-RAY DIFFRACTIONf_dihedral_angle_d14.0792671
X-RAY DIFFRACTIONf_chiral_restr0.051659
X-RAY DIFFRACTIONf_plane_restr0.006823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8288-1.87130.28461350.24822919X-RAY DIFFRACTION93
1.8713-1.91810.30381410.23863050X-RAY DIFFRACTION98
1.9181-1.970.28331420.23343055X-RAY DIFFRACTION97
1.97-2.0280.26541420.21393066X-RAY DIFFRACTION97
2.028-2.09340.23541410.19623046X-RAY DIFFRACTION97
2.0934-2.16820.24431400.18743027X-RAY DIFFRACTION96
2.1682-2.2550.22031400.18313020X-RAY DIFFRACTION96
2.255-2.35770.20651370.17362970X-RAY DIFFRACTION94
2.3577-2.4820.24521390.17323005X-RAY DIFFRACTION95
2.482-2.63740.20361420.16393044X-RAY DIFFRACTION96
2.6374-2.84110.18751410.16443046X-RAY DIFFRACTION96
2.8411-3.12690.17821380.15882999X-RAY DIFFRACTION94
3.1269-3.57920.19281380.15452963X-RAY DIFFRACTION92
3.5792-4.50880.15141400.1373038X-RAY DIFFRACTION94
4.5088-45.52540.16461430.15633090X-RAY DIFFRACTION91

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