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- PDB-6ub6: Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanas... -

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Basic information

Entry
Database: PDB / ID: 6ub6
TitleCrystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritetraose
ComponentsEndo-beta-1,3-glucanase
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyfungal-type cell wall polysaccharide metabolic process / : / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / fungal-type cell wall / Glycoside hydrolase superfamily / beta-laminaribiose / Endo-beta-1,3-glucanase
Function and homology information
Biological speciesLentinula edodes (shiitake mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSantos, C.R. / Lima, E.A. / Mandelli, F. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family.
Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8254
Polymers28,7811
Non-polymers1,0443
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.871, 47.678, 52.549
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-beta-1,3-glucanase


Mass: 28780.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinula edodes (shiitake mushroom) / Gene: glu1 / Production host: Escherichia coli (E. coli) / References: UniProt: G9M5R4
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate 5% dioxane 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 58956 / % possible obs: 99.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 10.54
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 5.6 % / Num. unique obs: 9283 / CC1/2: 0.659 / Rrim(I) all: 1.302 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→49.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.191 2927 5 %
Rwork0.174 --
obs-58538 99.6 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.199 Å20 Å20.448 Å2
2---0.811 Å20 Å2
3---0.218 Å2
Refinement stepCycle: LAST / Resolution: 1.25→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 69 383 2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132041
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171740
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.6842810
X-RAY DIFFRACTIONr_angle_other_deg3.0721.6044056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70724.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47415261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.406152
X-RAY DIFFRACTIONr_chiral_restr0.0620.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022272
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02418
X-RAY DIFFRACTIONr_nbd_refined0.1930.2405
X-RAY DIFFRACTIONr_nbd_other0.1890.258
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21018
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7681.31011
X-RAY DIFFRACTIONr_mcbond_other0.7681.31010
X-RAY DIFFRACTIONr_mcangle_it1.131.9541263
X-RAY DIFFRACTIONr_mcangle_other1.131.9551264
X-RAY DIFFRACTIONr_scbond_it1.0951.3611030
X-RAY DIFFRACTIONr_scbond_other1.0941.3611031
X-RAY DIFFRACTIONr_scangle_it1.5852.0161545
X-RAY DIFFRACTIONr_scangle_other1.5842.0161546
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.251-1.2830.3922130.3640540.36143060.6420.62799.09430.377
1.283-1.3180.3142100.30939960.30942160.780.79299.76280.307
1.318-1.3570.2632040.2538700.2540740.8390.8481000.244
1.357-1.3980.2811990.25937800.2639820.850.84399.92470.249
1.398-1.4440.261940.25136860.25138850.8570.87399.87130.239
1.444-1.4950.2271850.24935230.24837140.9030.89199.83840.231
1.495-1.5510.241790.20934020.2135860.9040.91799.86060.19
1.551-1.6140.1941750.1833110.1834860.9430.9451000.161
1.614-1.6860.1851660.17531570.17533240.9510.95299.96990.152
1.686-1.7680.1871610.16630530.16732150.9520.95599.96890.143
1.768-1.8640.171490.15528480.15630000.9560.96199.90.132
1.864-1.9770.2061420.19326960.19328970.9190.92797.96340.162
1.977-2.1130.1791350.15625550.15727020.9560.96499.55590.137
2.113-2.2820.1691250.14723830.14825330.9650.96899.0130.129
2.282-2.4990.1521150.1321880.13123120.9730.97599.61070.118
2.499-2.7930.1651060.13120090.13321150.9650.9751000.124
2.793-3.2240.153930.13717600.13818540.9720.97399.94610.134
3.224-3.9440.164780.13514940.13615860.9670.97699.11730.138
3.944-5.560.103620.1211750.11912380.9870.98299.91920.131
5.56-49.2480.295360.2176710.2217150.910.92398.88110.216

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