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- PDB-7dfq: Crystal Structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuro... -

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Basic information

Entry
Database: PDB / ID: 7dfq
TitleCrystal Structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase from Fusarium oxysporum 12S, ligand-free form
Components4-O-alpha-L-rhamnosyl-beta-D-glucuronidase
KeywordsHYDROLASE / TIM barrel / GH79 / beta-glucuronidase
Function / homologyGolgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 Å
AuthorsKondo, T. / Arakawa, T. / Fushinobu, S. / Sakamoto, T.
CitationJournal: Febs J. / Year: 2021
Title: Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum.
Authors: Kondo, T. / Kichijo, M. / Nakaya, M. / Takenaka, S. / Arakawa, T. / Kotake, T. / Fushinobu, S. / Sakamoto, T.
History
DepositionNov 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2063
Polymers50,7641
Non-polymers4422
Water9,188510
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint7 kcal/mol
Surface area16490 Å2
Unit cell
Length a, b, c (Å)42.431, 77.216, 126.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase


Mass: 50763.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Strain: 12S / Gene: FobglcA / Plasmid: pPICZ-alpha-A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: beta-glucuronidase
#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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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.: 510 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsThe amino acid sequence of 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase (FoBGlcA) has been registered ...The amino acid sequence of 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase (FoBGlcA) has been registered in GenBank, DDBj and EMBL. Its accession number is "LC534636".

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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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES-NaOH pH6.0, 30% (v/v) PEG mme 2000, 0.1M L-Rha, crystal was soaked into 20% glycerol at 298K for 1 min

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→65.86 Å / Num. obs: 68990 / % possible obs: 99.9 % / Redundancy: 6.47 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 39.4
Reflection shellResolution: 1.51→1.54 Å / Rmerge(I) obs: 0.575 / Num. unique obs: 3158 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.51→42.43 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3279 5 %RANDOM
Rwork0.1625 ---
obs0.1645 62631 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.99 Å2 / Biso mean: 20.313 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.51→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 28 510 3918
Biso mean--25.19 32.74 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023519
X-RAY DIFFRACTIONr_bond_other_d00.023162
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9444811
X-RAY DIFFRACTIONr_angle_other_deg3.97337290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12324.894141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50715501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.072159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214129
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02824
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 251 -
Rwork0.247 4491 -
all-4742 -
obs--99.33 %

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