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- PDB-7esn: Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase f... -

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Basic information

Entry
Database: PDB / ID: 7esn
TitleCrystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, H105F Rha-GlcA complex
ComponentsL-Rhamnose-alpha-1,4-D-glucuronate lyase
KeywordsLYASE / seven-bladed beta-propeller
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKondo, T. / Arakawa, T. / Fushinobu, S. / Sakamoto, T.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family.
Authors: Kondo, T. / Kichijo, M. / Maruta, A. / Nakaya, M. / Takenaka, S. / Arakawa, T. / Fushinobu, S. / Sakamoto, T.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _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: L-Rhamnose-alpha-1,4-D-glucuronate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0745
Polymers50,2941
Non-polymers7804
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-10 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.242, 190.137, 80.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-Rhamnose-alpha-1,4-D-glucuronate lyase


Mass: 50294.414 Da / Num. of mol.: 1 / Mutation: H105F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Strain: 12S / Gene: Forham1 / Plasmid: pPICZ-alpha-A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides

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Sugars , 2 types, 2 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
#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.: 1 / 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

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Non-polymers , 3 types, 146 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsThe amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession ...The amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession number is LC617219.

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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: 4.82 Å3/Da / Density % sol: 74.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.6 M ammonium sulfate, 0.1 M Na-acetate (pH 4.6), Crystal was soaked into 20 mM Rha-GlcA and 20 % (v/v) glycerol at 298 K for 1 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 8, 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: 2.42→105.75 Å / Num. obs: 37476 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 17.7
Reflection shellResolution: 2.42→2.51 Å / Num. unique obs: 3884 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→46.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.01 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1845 4.9 %RANDOM
Rwork0.2074 ---
obs0.209 35629 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.32 Å2 / Biso mean: 51.577 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å20 Å2
2---0.12 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 2.42→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 50 144 3665
Biso mean--73.99 49.64 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173238
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.6594915
X-RAY DIFFRACTIONr_angle_other_deg1.1321.5987483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4055434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77723.316196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53315574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6391517
X-RAY DIFFRACTIONr_chiral_restr0.0480.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
LS refinement shellResolution: 2.42→2.483 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 133 -
Rwork0.374 2585 -
all-2718 -
obs--99.89 %

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