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- PDB-6ub1: Crystal structure of a GH128 (subgroup III) curdlan-specific exo-... -

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Entry
Database: PDB / ID: 6ub1
TitleCrystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III) in complex with laminaribiose at -3 and -2 subsites
ComponentsGLYCOSIDE HYDROLASE
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 / beta-D-glucopyranose / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesBlastomyces gilchristii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSIDE HYDROLASE
B: GLYCOSIDE HYDROLASE
C: GLYCOSIDE HYDROLASE
D: GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1808
Polymers111,9734
Non-polymers1,2074
Water19,7441096
1
A: GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3352
Polymers27,9931
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1732
Polymers27,9931
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3352
Polymers27,9931
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3352
Polymers27,9931
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.323, 60.804, 63.545
Angle α, β, γ (deg.)69.670, 78.240, 77.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GLYCOSIDE HYDROLASE /


Mass: 27993.135 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces gilchristii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179UGT5
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 3 / Source method: isolated from a natural 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
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1096 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.76 Å3/Da / Density % sol: 30.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: 1.45854 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45854 Å / Relative weight: 1
ReflectionResolution: 1.6→35.49 Å / Num. obs: 87019 / % possible obs: 86.2 % / Redundancy: 3.3 % / CC1/2: 0.994 / Net I/σ(I): 13.35
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.48 / Num. unique obs: 14093 / CC1/2: 0.986 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UAY

6uay


Resolution: 1.6→35.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.068 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 4350 5 %RANDOM
Rwork0.1604 ---
obs0.1623 82649 86.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.63 Å2 / Biso mean: 16.249 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.25 Å2-0.27 Å2
2--0.68 Å2-0.32 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.6→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6988 0 81 1096 8165
Biso mean--27.2 27.46 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176418
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.659976
X-RAY DIFFRACTIONr_angle_other_deg1.5991.58814896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.2295.425954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12623.239352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.832151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6681527
X-RAY DIFFRACTIONr_chiral_restr0.1060.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021630
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 314 -
Rwork0.156 5982 -
all-6296 -
obs--84.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43550.15410.15730.33130.14270.08710.0111-0.05880.02190.0071-0.0118-0.00430.0115-0.00870.00070.02260.0059-0.00060.0494-0.0040.0024-21.658333.3803-52.9874
20.23750.0953-0.14240.12360.09310.3689-0.01910.00680.00590.00060.00930.01780.02910.01790.00980.03010.00740.0050.01060.00260.02181.58663.678-51.3044
30.54810.1510.13860.11890.1780.35290.00170.0846-0.03690.02330.0189-0.00510.00070.0216-0.02070.0336-0.00150.00980.0188-0.01030.01591.583-15.6281-22.2162
40.27050.02470.0330.35050.11450.04560.0277-0.020.00650.016-0.0281-0.0070.0070.00470.00040.0269-0.0040.00410.04370.00750.0023-21.60514.1558-23.6733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 302
2X-RAY DIFFRACTION2B33 - 301
3X-RAY DIFFRACTION3C33 - 302
4X-RAY DIFFRACTION4D33 - 302

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