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- PDB-6ubb: Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase... -

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Basic information

Entry
Database: PDB / ID: 6ubb
TitleCrystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) with laminaribiose at the surface-binding site
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 / beta-laminaribiose / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesAureobasidium namibiae CBS 147.97 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSantos, C.R. / Vieira, P.S. / Domingues, M.N. / Cordeiro, R.L. / Tomazini, A. / 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 / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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 2.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Glyco_hydro_cc domain-containing protein
B: Glyco_hydro_cc domain-containing protein
C: Glyco_hydro_cc domain-containing protein
D: Glyco_hydro_cc domain-containing protein
E: Glyco_hydro_cc domain-containing protein
F: Glyco_hydro_cc domain-containing protein
G: Glyco_hydro_cc domain-containing protein
H: Glyco_hydro_cc domain-containing protein
I: Glyco_hydro_cc domain-containing protein
J: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,53420
Polymers308,11110
Non-polymers3,42310
Water8,593477
1
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers30,8111
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.349, 152.733, 169.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glyco_hydro_cc domain-containing protein


Mass: 30811.098 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aureobasidium namibiae CBS 147.97 (fungus)
Gene: M436DRAFT_66913 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A074W9U7
#2: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 10
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.18 M tri-ammonium citrate, 18% v/v PEG 3,350, 0.01 M Cobalt (II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45857 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45857 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 130821 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.98 / Net I/σ(I): 4.8
Reflection shellResolution: 2.35→2.49 Å / Num. unique obs: 20840 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: FREE R-VALUE / ESU R: 0.458 / ESU R Free: 0.296
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.301 6541 5 %
Rwork0.265 --
obs-130808 99.8 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.831 Å20 Å20 Å2
2---2.842 Å20 Å2
3----0.989 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20310 0 230 477 21017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01321230
X-RAY DIFFRACTIONr_bond_other_d0.0350.01718847
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.65328893
X-RAY DIFFRACTIONr_angle_other_deg2.4741.59143937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53452462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25522.7271100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.859153541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21215100
X-RAY DIFFRACTIONr_chiral_restr0.0420.22681
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223224
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024492
X-RAY DIFFRACTIONr_nbd_refined0.1650.24040
X-RAY DIFFRACTIONr_nbd_other0.1620.2129
X-RAY DIFFRACTIONr_nbtor_refined0.1550.29837
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2642
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_it0.473.6979878
X-RAY DIFFRACTIONr_mcbond_other0.473.6979877
X-RAY DIFFRACTIONr_mcangle_it0.8825.54412330
X-RAY DIFFRACTIONr_mcangle_other0.8825.54412331
X-RAY DIFFRACTIONr_scbond_it0.2913.66411352
X-RAY DIFFRACTIONr_scbond_other0.2913.66411353
X-RAY DIFFRACTIONr_scangle_it0.5565.48216563
X-RAY DIFFRACTIONr_scangle_other0.5565.48216564
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
2.35-2.4110.3854750.38190290.38195510.4430.47199.50790.367
2.411-2.4770.3764660.37388450.37493360.5060.51999.73220.358
2.477-2.5480.4034520.36285960.36490650.5220.55599.81250.342
2.548-2.6270.3734410.34783680.34888220.6330.64899.85260.323
2.627-2.7130.3554280.3381450.33185790.6940.69799.93010.299
2.713-2.8070.3414150.31678740.31882910.7370.73699.97590.285
2.807-2.9130.3443990.30975930.3179980.7270.76199.9250.277
2.913-3.0320.3453860.28673300.28977200.7770.80999.94820.25
3.032-3.1660.3093700.28770280.28974020.8230.82599.9460.254
3.166-3.320.3173550.26467390.26670950.8230.85499.98590.231
3.32-3.4980.33380.25664260.25967640.8660.8811000.23
3.498-3.7090.2733200.22560780.22763980.8950.9161000.201
3.709-3.9640.263010.20957200.21160230.9120.92399.96680.181
3.964-4.2790.2432820.19953580.20156410.9240.93499.98230.172
4.279-4.6840.2262600.19949420.252060.9390.9499.92320.167
4.684-5.2310.2452360.19944850.20147300.9370.94199.80970.167
5.231-6.0290.2692100.22839920.2342080.9150.92799.85740.189
6.029-7.3570.2651800.22934200.23136010.9210.92199.97220.193
7.357-10.290.2281430.20527050.20628490.9470.95199.96490.188
10.29-49.2990.35840.31115940.31317090.8950.92498.18610.289

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