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- PDB-6ub0: Crystal structure of a GH128 (subgroup III) curdlan-specific exo-... -

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Basic information

Entry
Database: PDB / ID: 6ub0
TitleCrystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III) in complex with laminaribiose at -2 and -1 subsites
ComponentsGlyco_hydro_cc domain-containing protein
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 / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesBlastomyces gilchristii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCosta, P.A.C.R. / Santos, C.R. / Domingues, M.N. / 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_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.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 / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 30, 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

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Assembly

Deposited unit
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0392
Polymers24,6971
Non-polymers3421
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.561, 34.231, 56.351
Angle α, β, γ (deg.)90.000, 104.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 24696.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces gilchristii (strain SLH14081) (fungus)
Strain: SLH14081 / Gene: BDBG_03339 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179UGT5
#2: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Potassium di-hydrogen phosphate 24% Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45855 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45855 Å / Relative weight: 1
ReflectionResolution: 1.75→32.11 Å / Num. obs: 18575 / % possible obs: 98.9 % / Redundancy: 4.61 % / CC1/2: 0.999 / Net I/σ(I): 24.65
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 4.14 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2873 / CC1/2: 0.976 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UAY

6uay


Resolution: 1.75→32.11 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.04 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 929 5 %RANDOM
Rwork0.2203 ---
obs0.2226 17645 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.5 Å2 / Biso mean: 33.877 Å2 / Biso min: 16.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å2-0 Å20.72 Å2
2---0.4 Å20 Å2
3----1.82 Å2
Refinement stepCycle: final / Resolution: 1.75→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 23 48 1818
Biso mean--34.04 37.44 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131834
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171605
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.6522500
X-RAY DIFFRACTIONr_angle_other_deg1.4471.5893728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5255231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33823.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.779157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02403
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 63 -
Rwork0.29 1193 -
all-1256 -
obs--91.75 %
Refinement TLS params.Method: refined / Origin x: 8.308 Å / Origin y: 0.36 Å / Origin z: 14.141 Å
111213212223313233
T0.0706 Å20.0417 Å2-0.0074 Å2-0.1274 Å2-0.018 Å2--0.0298 Å2
L2.1706 °2-0.0511 °2-1.3341 °2-0.0899 °2-0.3227 °2--3.2272 °2
S-0.0253 Å °-0.1618 Å °0.0655 Å °-0.0696 Å °-0.0723 Å °-0.0153 Å °0.2449 Å °0.0285 Å °0.0976 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 262
2X-RAY DIFFRACTION1A301 - 302

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