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- PDB-6la0: Crystal structure of AoRut -

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Basic information

Entry
Database: PDB / ID: 6la0
TitleCrystal structure of AoRut
ComponentsGlycoside hydrolase family 5
KeywordsHYDROLASE / AoRut / CARBOHYDRATE
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
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKoseki, T. / Makabe, K.
CitationJournal: Appl.Environ.Microbiol. / Year: 2021
Title: Aspergillus oryzae Rutinosidase: Biochemical and Structural Investigation.
Authors: Makabe, K. / Hirota, R. / Shiono, Y. / Tanaka, Y. / Koseki, T.
History
DepositionNov 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 5
B: Glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,71612
Polymers83,5042
Non-polymers2,21210
Water15,781876
1
A: Glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8586
Polymers41,7521
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8586
Polymers41,7521
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.908, 169.989, 50.485
Angle α, β, γ (deg.)90.000, 115.619, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycoside hydrolase family 5 / AoRut


Mass: 41752.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01080470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DRB1
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 12% PEG4000, 0.5 M NaAcetate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 72840 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 20.93 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.28
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 11345 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.152refinement
XDSdata processing
Cootmodel building
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pf0

2pf0


Resolution: 1.75→19.57 Å / SU ML: 0.2618 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 3565 4.91 %
Rwork0.1958 69110 -
obs0.1975 72675 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 140 876 6718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076014
X-RAY DIFFRACTIONf_angle_d0.81468210
X-RAY DIFFRACTIONf_chiral_restr0.0544886
X-RAY DIFFRACTIONf_plane_restr0.00571060
X-RAY DIFFRACTIONf_dihedral_angle_d15.92412090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.44081260.3672660X-RAY DIFFRACTION96.67
1.77-1.80.36151390.31242764X-RAY DIFFRACTION99.9
1.8-1.830.34541490.28812743X-RAY DIFFRACTION99.93
1.83-1.850.32541590.26882782X-RAY DIFFRACTION100
1.85-1.890.3121590.25482722X-RAY DIFFRACTION99.93
1.89-1.920.27071370.22662777X-RAY DIFFRACTION100
1.92-1.950.24761180.22262788X-RAY DIFFRACTION99.93
1.95-1.990.27221350.21272780X-RAY DIFFRACTION99.97
1.99-2.030.29741530.22012769X-RAY DIFFRACTION99.86
2.03-2.070.26621210.21542777X-RAY DIFFRACTION99.83
2.07-2.120.24761210.20612775X-RAY DIFFRACTION99.83
2.12-2.180.25571330.19492809X-RAY DIFFRACTION99.7
2.18-2.230.27391530.19672674X-RAY DIFFRACTION99.72
2.23-2.30.22981780.20992808X-RAY DIFFRACTION99.8
2.3-2.370.27851570.20172737X-RAY DIFFRACTION99.79
2.37-2.460.25911770.21112706X-RAY DIFFRACTION99.76
2.46-2.560.26591460.19852768X-RAY DIFFRACTION99.83
2.56-2.670.23261520.20132794X-RAY DIFFRACTION99.9
2.67-2.810.23621390.19732784X-RAY DIFFRACTION99.73
2.81-2.990.24311390.19062735X-RAY DIFFRACTION99.58
2.99-3.220.21431360.1922782X-RAY DIFFRACTION99.56
3.22-3.540.19591160.18372791X-RAY DIFFRACTION99.69
3.54-4.050.15451130.16722819X-RAY DIFFRACTION99.9
4.05-5.090.16691350.15472789X-RAY DIFFRACTION99.83
5.09-19.570.18691740.16512777X-RAY DIFFRACTION99.86

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