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

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Basic information

Entry
Database: PDB / ID: 7esk
TitleCrystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, Ligand free form
ComponentsL-Rhamnose-alpha-1,4-D-glucuronate lyase
KeywordsLYASE / seven-bladed beta-propeller
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 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 1.2Nov 13, 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)50,8974
Polymers50,0851
Non-polymers8123
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-1 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.113, 65.267, 107.008
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 L-Rhamnose-alpha-1,4-D-glucuronate lyase


Mass: 50085.199 Da / Num. of mol.: 1
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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % (v/v) PEG 1500, 0.1 M BICINE-NaOH (pH 8.5), 10 % (v/v) 2-propanol, Crystal was soaked into 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: Mar 2, 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: 1.05→50 Å / Num. obs: 190044 / % possible obs: 94.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 39.4
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 9391 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.05→31.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.389 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 9565 5 %RANDOM
Rwork0.1505 ---
obs0.1515 179860 99.9 %-
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: 54.71 Å2 / Biso mean: 16.018 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.05→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 52 597 3986
Biso mean--27.98 26.89 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193517
X-RAY DIFFRACTIONr_bond_other_d0.0020.023167
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9544793
X-RAY DIFFRACTIONr_angle_other_deg1.137323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02424.483174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2315554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6591517
X-RAY DIFFRACTIONr_chiral_restr0.1380.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024004
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02835
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 732 -
Rwork0.262 13134 -
all-13866 -
obs--99.83 %

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