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

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Basic information

Entry
Database: PDB / ID: 7dfs
TitleCrystal structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase from Fusarium oxysporum 12S - Rha-GlcA complex
Components4-O-alpha-L-rhamnosyl-beta-D-glucuronidase
KeywordsHYDROLASE / TIM barrel / antiparallel beta-sheet
Function / homologyGolgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta / alpha-D-mannopyranose
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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

Downloads & links

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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)52,0676
Polymers50,7641
Non-polymers1,3035
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint15 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.682, 78.567, 127.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Non-polymers , 2 types, 547 molecules A

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 5 molecules

#2: Polysaccharide alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 340.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122A-1b_1-5][a2211m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-rhamnopyranose-(1-4)-alpha-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 340.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-4DGlcpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122A-1a_1-5][a2211m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpA]{[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#4: 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
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% (v/v) PEG mme 2000, 0.1 M MES-NaOH (pH 6.0), crystal was soaked into 20 mM Rha-GlcA and 20% glycerol at 298K for 5 min

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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 S 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→49.54 Å / Num. obs: 70690 / % possible obs: 99.6 % / Redundancy: 4.54 % / CC1/2: 0.996 / Net I/σ(I): 23.1
Reflection shellResolution: 1.49→1.52 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3478 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FoBGlcA ligand-free

Resolution: 1.49→49.49 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 3549 5 %RANDOM
Rwork0.1463 ---
obs0.1478 67062 99.57 %-
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: 69.43 Å2 / Biso mean: 22.45 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.49→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 85 546 4011
Biso mean--26.86 35.26 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023581
X-RAY DIFFRACTIONr_bond_other_d00.023202
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9654901
X-RAY DIFFRACTIONr_angle_other_deg3.91137397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44624.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10915504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0771510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214128
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02822
LS refinement shellResolution: 1.49→1.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 261 -
Rwork0.261 4897 -
all-5158 -
obs--99.79 %

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