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

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Basic information

Entry
Database: PDB / ID: 7yqs
TitleNeutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex
ComponentsL-RHAMNOSE-ALPHA-1,4-D-GLUCURONATE LYASE
KeywordsLYASE / neutron diffraction crystallography / polysaccharide lyase / gum arabic / carbohydrate-active enzyme
Function / homologyACETATE ION / alpha-L-rhamnopyranose
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
DepositionAug 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / software
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.title / _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

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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
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint15 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.780, 65.800, 108.950
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) / Production host: Komagataella pastoris (fungus)

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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: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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, 303 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: isolated from a natural source / 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.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Details: 8.5(pD) / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution : protein 24mg/ml, 20mM Tris-DCl (pD 8.0), Reservoir solution : 33 % (w/v) PEG 1500, 0.1 M Tris-DCl (pD 8.5), 0.1 M L-Rha

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1293room temperature1N
2293room temperature1N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.28-6.19
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 S 6M1PIXELMar 17, 2021
iBIX2DIFFRACTOMETERFeb 12, 2021
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.281
36.191
Reflection

Biso Wilson estimate: 14.58 Å2 / Entry-ID: 7YQS

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.25-43.421153881006.40.9990.0590.025115
1.8-19.823882698.9-37.90.9830.2570.09628.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.25-1.276.40.8862.256670.7940.381100
1.8-1.865.91.1741.638250.4110.507298

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
Refinement

SU ML: 0.1148 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 16.6944 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 7esk

7esk

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.25-43.42X-RAY DIFFRACTION33.310.1630.14650.14745764109527115291599.9611.33
1.8-19.82NEUTRON DIFFRACTION0.19070.16190.16341946388245.01992
Refinement stepCycle: LAST / Resolution: 1.25→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 108 299 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717556
X-RAY DIFFRACTIONf_angle_d1.160313232
X-RAY DIFFRACTIONf_chiral_restr0.0911529
X-RAY DIFFRACTIONf_plane_restr0.00581482
X-RAY DIFFRACTIONf_dihedral_angle_d15.24642110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.23961890.25543594X-RAY DIFFRACTION99.74
1.26-1.280.29311890.24723597X-RAY DIFFRACTION99.97
1.28-1.290.26441900.24443617X-RAY DIFFRACTION99.95
1.29-1.310.24151900.2343620X-RAY DIFFRACTION100
1.31-1.330.26211900.22223605X-RAY DIFFRACTION99.97
1.33-1.350.21421910.2183631X-RAY DIFFRACTION100
1.35-1.370.19961900.21063607X-RAY DIFFRACTION100
1.37-1.390.22121900.20383613X-RAY DIFFRACTION100
1.39-1.410.20821910.19473611X-RAY DIFFRACTION100
1.41-1.430.20571910.18983643X-RAY DIFFRACTION100
1.43-1.460.21011900.18113600X-RAY DIFFRACTION99.97
1.46-1.480.18951920.17823654X-RAY DIFFRACTION100
1.48-1.510.19891890.17093590X-RAY DIFFRACTION99.97
1.51-1.540.20261910.16423619X-RAY DIFFRACTION99.97
1.54-1.570.17551890.16363618X-RAY DIFFRACTION99.97
1.57-1.610.17031940.1613671X-RAY DIFFRACTION99.97
1.61-1.650.18461920.15883647X-RAY DIFFRACTION100
1.65-1.70.17921890.15493601X-RAY DIFFRACTION100
1.7-1.750.16431930.14973650X-RAY DIFFRACTION100
1.75-1.80.13911920.14663644X-RAY DIFFRACTION100
1.8-1.870.15621920.14153665X-RAY DIFFRACTION100
1.87-1.940.15511920.13653653X-RAY DIFFRACTION100
1.94-2.030.15181930.13453642X-RAY DIFFRACTION100
2.03-2.140.1511930.13263690X-RAY DIFFRACTION100
2.14-2.270.15551930.1383655X-RAY DIFFRACTION99.95
2.27-2.450.14791950.13773695X-RAY DIFFRACTION100
2.45-2.690.17711940.13783694X-RAY DIFFRACTION100
2.69-3.080.13661960.13913724X-RAY DIFFRACTION99.97
3.08-3.880.14441990.12713773X-RAY DIFFRACTION99.85
3.88-43.420.14952050.12923904X-RAY DIFFRACTION99.61

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