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- PDB-4i3g: Crystal Structure of DesR, a beta-glucosidase from Streptomyces v... -

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Basic information

Entry
Database: PDB / ID: 4i3g
TitleCrystal Structure of DesR, a beta-glucosidase from Streptomyces venezuelae in complex with D-glucose.
ComponentsBeta-glucosidase
KeywordsHYDROLASE / PA14 Domain / beta-glucosidase / Macrolide antibiotic / Antibiotic activation / Extracellular
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Jelly Rolls - #380 / Glycoside 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, N-terminal domain / PA14 / PA14 domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain ...Jelly Rolls - #380 / Glycoside 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, N-terminal domain / PA14 / PA14 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 / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZmudka, M.W. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2013
Title: The structure of DesR from Streptomyces venezuelae, a beta-glucosidase involved in macrolide activation.
Authors: Zmudka, M.W. / Thoden, J.B. / Holden, H.M.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: 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
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,27922
Polymers174,1002
Non-polymers2,18020
Water27,7611541
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,33213
Polymers87,0501
Non-polymers1,28212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9489
Polymers87,0501
Non-polymers8988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.269, 198.314, 67.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-glucosidase /


Mass: 87049.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: desR / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: C5IXN7
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1559 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1541 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3 M ammonium sulfate, 300 mM potassium chloride, 25 mM glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 324839 / Num. obs: 324839 / % possible obs: 94.1 % / Redundancy: 6.4 %
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 32626 / Rsym value: 0.38 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AC0

3ac0


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.898 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19876 16375 5 %RANDOM
Rwork0.17202 ---
obs0.17336 308445 94.65 %-
all-324820 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.206 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11537 0 126 1541 13204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211924
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.96816259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59151570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57824.509479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.532151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0621570
X-RAY DIFFRACTIONr_chiral_restr0.130.21840
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219090
X-RAY DIFFRACTIONr_mcbond_it1.5061.57745
X-RAY DIFFRACTIONr_mcangle_it2.314212401
X-RAY DIFFRACTIONr_scbond_it3.43134179
X-RAY DIFFRACTIONr_scangle_it5.334.53851
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 1186 -
Rwork0.248 22618 -
obs--94.65 %

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