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- PDB-8i4d: X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase fro... -

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Basic information

Entry
Database: PDB / ID: 8i4d
TitleX-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex at 100K
ComponentsL-Rhamnose-alpha-1,4-D-glucuronate lyase
KeywordsLYASE / polysaccharide lyase / gum arabic / carbohydrate-active enzyme
Function / homologyBNR repeat-containing family member / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / metal ion binding / ACETATE ION / alpha-L-rhamnopyranose / L-Rhamnose-alpha-1,4-D-glucuronate lyase
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsYano, N. / Kondo, T. / Kusaka, K. / Yamada, T. / Arakawa, T. / Sakamoto, T. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H00929 Japan
Japan Society for the Promotion of Science (JSPS)15H02443 Japan
Japan Society for the Promotion of Science (JSPS)26660083 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography.
Authors: Yano, N. / Kondo, T. / Kusaka, K. / Arakawa, T. / Sakamoto, T. / Fushinobu, S.
History
DepositionJan 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 6, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 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

Downloads & links

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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)51,7297
Polymers50,0851
Non-polymers1,6446
Water8,251458
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.313, 65.230, 108.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 50085.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: Forham1 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A8J0PCK3, EC: 4.2.2.28

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 462 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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 / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PROTEIN SOLUTION : PROTEIN 24MG/ML, 20MM TRIS-DCL (PD 8.0), RESERVOIR SOLUTION : 36 % (W/V) PEG 1500, 0.1 M TRIS-DCL (PD 8.5), 0.1 M L-RHA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→42.63 Å / Num. obs: 180680 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 11.9
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8886 / CC1/2: 0.814 / Rpim(I) all: 0.323 / Rrim(I) all: 1.124 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YQS

7yqs


Resolution: 1.06→41.65 Å / SU ML: 0.088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1829 8948 4.96 %
Rwork0.1718 171584 -
obs0.1723 180532 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.22 Å2
Refinement stepCycle: LAST / Resolution: 1.06→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 108 458 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473638
X-RAY DIFFRACTIONf_angle_d0.90374963
X-RAY DIFFRACTIONf_chiral_restr0.0869543
X-RAY DIFFRACTIONf_plane_restr0.0062641
X-RAY DIFFRACTIONf_dihedral_angle_d13.38041360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.070.26882840.25565673X-RAY DIFFRACTION99.97
1.07-1.080.25683150.24695646X-RAY DIFFRACTION100
1.08-1.10.24552730.23845691X-RAY DIFFRACTION100
1.1-1.110.25243180.23345610X-RAY DIFFRACTION100
1.11-1.130.22312790.22395710X-RAY DIFFRACTION99.98
1.13-1.140.22923000.22175656X-RAY DIFFRACTION99.98
1.14-1.160.2252760.21585680X-RAY DIFFRACTION100
1.16-1.180.22943320.21415649X-RAY DIFFRACTION99.98
1.18-1.190.20913010.20775670X-RAY DIFFRACTION99.98
1.19-1.210.20842980.2015688X-RAY DIFFRACTION100
1.21-1.230.20622700.19595703X-RAY DIFFRACTION99.98
1.23-1.260.21733040.19695672X-RAY DIFFRACTION100
1.26-1.280.19182820.19645705X-RAY DIFFRACTION99.97
1.28-1.310.21982880.19535675X-RAY DIFFRACTION99.98
1.31-1.340.2142930.19015682X-RAY DIFFRACTION99.95
1.34-1.370.2262830.19135727X-RAY DIFFRACTION100
1.37-1.40.18962880.18365667X-RAY DIFFRACTION99.92
1.4-1.440.17953010.18255722X-RAY DIFFRACTION99.93
1.44-1.480.19132890.17365706X-RAY DIFFRACTION99.93
1.48-1.530.17963060.17155700X-RAY DIFFRACTION99.97
1.53-1.580.18152910.17075727X-RAY DIFFRACTION99.98
1.58-1.650.17613000.16315735X-RAY DIFFRACTION99.93
1.65-1.720.17333290.16535681X-RAY DIFFRACTION99.97
1.72-1.810.192900.16515754X-RAY DIFFRACTION99.97
1.81-1.930.16813050.16595748X-RAY DIFFRACTION100
1.93-2.070.16943090.16275748X-RAY DIFFRACTION99.92
2.07-2.280.172970.15985791X-RAY DIFFRACTION99.93
2.28-2.610.18423130.16775816X-RAY DIFFRACTION99.95
2.61-3.290.17693030.16255880X-RAY DIFFRACTION99.9
3.29-41.650.15773310.1476072X-RAY DIFFRACTION99.95

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