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- PDB-6i1a: Crystal structure of rutinosidase from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 6i1a
TitleCrystal structure of rutinosidase from Aspergillus niger
Componentsrutinosidase
KeywordsHYDROLASE / glycosyl hydrolase / carbohydrate biotechnology
Function / homology
Function and homology information


glucan 1,3-beta-glucosidase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
glucan 1,3-beta-glucosidase / glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.27 Å
AuthorsPachl, P. / Rezacova, P. / Kapesova, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation18-00150S Czech Republic
CitationJournal: Febs J. / Year: 2020
Title: Rutinosidase from Aspergillus niger: crystal structure and insight into the enzymatic activity.
Authors: Pachl, P. / Kapesova, J. / Brynda, J. / Biedermannova, L. / Pelantova, H. / Bojarova, P. / Kren, V. / Rezacova, P. / Kotik, M.
History
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine / 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 / _refine.pdbx_diffrn_id / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: rutinosidase
B: rutinosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,28640
Polymers83,3362
Non-polymers3,95038
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint127 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.068, 97.359, 139.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rutinosidase


Mass: 41667.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: ATCC64974_105530 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A254TQT9, UniProt: G3YFQ1*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.5
Details: 20 mM Amonium Sulfate, 0.1 M Bis-Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 180049 / % possible obs: 94.6 % / Redundancy: 2.98 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 9.58
Reflection shellResolution: 1.27→1.35 Å / Redundancy: 2.19 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 22781 / CC1/2: 0.359 / Rrim(I) all: 1.446 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.27→46.6 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17822 1801 1 %RANDOM
Rwork0.1593 ---
obs0.15949 178251 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.629 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.53 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.27→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 252 684 6652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136176
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175309
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6828396
X-RAY DIFFRACTIONr_angle_other_deg2.381.59612341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28223.75312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08915879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9581517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026890
X-RAY DIFFRACTIONr_gen_planes_other0.0230.021352
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_it1.3171.522874
X-RAY DIFFRACTIONr_mcbond_other1.3141.5192873
X-RAY DIFFRACTIONr_mcangle_it1.8022.2793592
X-RAY DIFFRACTIONr_mcangle_other1.8042.2793593
X-RAY DIFFRACTIONr_scbond_it2.7391.8133302
X-RAY DIFFRACTIONr_scbond_other2.7381.8143303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9152.624799
X-RAY DIFFRACTIONr_long_range_B_refined4.63319.2977229
X-RAY DIFFRACTIONr_long_range_B_other4.63519.3017230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 95 -
Rwork0.363 9402 -
obs--68.19 %

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