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- PDB-5c71: The structure of Aspergillus oryzae a-glucuronidase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 5c71
TitleThe structure of Aspergillus oryzae a-glucuronidase complexed with glycyrrhetinic acid monoglucuronide
ComponentsGlucuronidase
KeywordsHYDROLASE / beta-glucuronidase / glycyrrhetinic acid monoglucuronide
Function / homology
Function and homology information


beta-mannosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CBW / alpha-D-glucopyranuronic acid / beta-mannosidase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsSun, H.L. / Lv, B. / Huang, S. / Li, C. / Jiang, T.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Structure-guided engineering of the substrate specificity of a fungal beta-glucuronidase toward triterpenoid saponins.
Authors: Lv, B. / Sun, H. / Huang, S. / Feng, X. / Jiang, T. / Li, C.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 1, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / entity / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec / _entity.pdbx_mutation / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucuronidase
B: Glucuronidase
C: Glucuronidase
D: Glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,3118
Polymers284,9814
Non-polymers1,3304
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-81 kcal/mol
Surface area78490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.068, 96.231, 96.192
Angle α, β, γ (deg.)88.270, 74.360, 71.130
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glucuronidase /


Mass: 71245.359 Da / Num. of mol.: 4 / Mutation: E414D, E505D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Strain: Li-3 / Gene: Pgus / Plasmid: PET28A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A7XS03, beta-mannosidase
#2: Chemical ChemComp-CBW / (3BETA,5BETA,14BETA)-3-HYDROXY-11-OXOOLEAN-12-EN-29-OIC ACID / Enoxolone


Mass: 470.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H46O4 / Comment: antiinflammatory*YM
#3: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS EU095019.1 FOR THIS SEQUENCE. N-TERMINAL RESIDUES MGSSHHHHHHSSGLVPRGSHMASMTGGQQGRGS ARE EXPRESSION TAGS.

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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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1M Succinic acid / PH range: 6.9-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 92474 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.23 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.925 / Net I/av σ(I): 24.386 / Net I/σ(I): 13 / Num. measured all: 362238
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.61-2.663.90.15744360.8293.4
2.66-2.73.90.15545490.85498.1
2.7-2.7640.14646560.83898.1
2.76-2.8140.12746300.84498.3
2.81-2.873.90.11646060.89698.3
2.87-2.943.90.10246350.9398.4
2.94-3.013.90.09246620.92998.4
3.01-3.093.90.08546440.94998.5
3.09-3.193.90.07346560.9698.6
3.19-3.293.90.06646260.96898.4
3.29-3.413.90.0646250.95798.8
3.41-3.543.90.05446741.01598.5
3.54-3.73.90.0546071.01698.7
3.7-3.93.90.04746060.99198.7
3.9-4.143.90.04347140.9698.8
4.14-4.463.90.04146310.9698.9
4.46-4.913.90.0446410.96698.8
4.91-5.623.90.04346491.0298.5
5.62-7.083.90.04445820.87397.8
7.08-503.80.03146450.74798.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data scaling
HKL-2000data processing
AMoREphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C70

5c70


Resolution: 2.62→46.226 Å / FOM work R set: 0.825 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 4537 4.91 %
Rwork0.1869 87791 -
obs0.1899 92328 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.21 Å2 / Biso mean: 14.51 Å2 / Biso min: 0.28 Å2
Refinement stepCycle: final / Resolution: 2.62→46.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18572 0 92 180 18844
Biso mean--65.22 11.76 -
Num. residues----2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01419156
X-RAY DIFFRACTIONf_angle_d1.74726128
X-RAY DIFFRACTIONf_chiral_restr0.0962866
X-RAY DIFFRACTIONf_plane_restr0.0083374
X-RAY DIFFRACTIONf_dihedral_angle_d15.1926814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6197-2.64950.35481410.2342647278888
2.6495-2.68060.30681430.22082973311698
2.6806-2.71330.30821520.22142870302298
2.7133-2.74770.30241420.2182980312298
2.7477-2.78380.31041280.2222891301998
2.7838-2.82190.30351720.21052947311998
2.8219-2.86220.30811590.21852899305898
2.8622-2.9050.31121570.20782988314598
2.905-2.95040.28291460.2142892303898
2.9504-2.99870.29471800.21152980316098
2.9987-3.05040.33251410.21752893303498
3.0504-3.10590.29981500.22092990314099
3.1059-3.16560.27451360.20762903303998
3.1656-3.23020.28231430.19712977312098
3.2302-3.30040.271540.1962944309898
3.3004-3.37720.28641520.21152918307099
3.3772-3.46160.2751610.19572952311399
3.4616-3.55520.25521590.18782982314199
3.5552-3.65970.25521470.18152903305099
3.6597-3.77780.22131600.17942904306499
3.7778-3.91280.21721660.16812933309999
3.9128-4.06930.20971460.16612959310599
4.0693-4.25440.20041360.15312983311999
4.2544-4.47850.1661480.14312976312499
4.4785-4.75890.18921740.14632929310399
4.7589-5.12590.20051590.16012941310099
5.1259-5.64090.21971260.16852970309698
5.6409-6.45530.23531660.18822924309098
6.4553-8.12570.1971490.18282876302597
8.1257-46.23280.17261440.16352867301196

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