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- PDB-6ub5: Crystal structure (P21 form) of a GH128 (subgroup IV) endo-beta-1... -

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Basic information

Entry
Database: PDB / ID: 6ub5
TitleCrystal structure (P21 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose
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: 1.3 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 2.2Nov 13, 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)29,6634
Polymers28,7811
Non-polymers8823
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.806, 47.710, 52.517
Angle α, β, γ (deg.)90.000, 110.810, 90.000
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


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][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.: 355 / 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: 1.86 Å3/Da / Density % sol: 34.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: lithium sulfate 1.4 M 2% PEG400 Tris 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.03312 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03312 Å / Relative weight: 1
ReflectionResolution: 1.3→49.09 Å / Num. obs: 52180 / % possible obs: 99.8 % / Redundancy: 5.85 % / CC1/2: 0.995 / Net I/σ(I): 7.42
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 8384 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→49.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.052
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 2609 5 %RANDOM
Rwork0.1686 ---
obs0.1692 49571 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 46.31 Å2 / Biso mean: 8.978 Å2 / Biso min: 5.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0.04 Å2
2---0.43 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.3→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 58 355 2304
Biso mean--14.11 22.67 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132043
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171745
X-RAY DIFFRACTIONr_angle_refined_deg1.251.6752813
X-RAY DIFFRACTIONr_angle_other_deg2.3591.5974069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18424.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.47152
X-RAY DIFFRACTIONr_chiral_restr0.060.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02422
X-RAY DIFFRACTIONr_mcbond_it0.5820.821020
X-RAY DIFFRACTIONr_mcbond_other0.5780.821019
X-RAY DIFFRACTIONr_mcangle_it0.9551.2321279
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 191 -
Rwork0.268 3640 -
all-3831 -
obs--99.79 %

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