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- PDB-6ub8: Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase... -

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Basic information

Entry
Database: PDB / ID: 6ub8
TitleCrystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI)
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 speciesAureobasidium namibiae CBS 147.97 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 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 1.2Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)311,15043
Polymers308,11110
Non-polymers3,03933
Water20,5371140
1
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0874
Polymers30,8111
Non-polymers2763
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)31,0874
Polymers30,8111
Non-polymers2763
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)30,9953
Polymers30,8111
Non-polymers1842
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)31,0874
Polymers30,8111
Non-polymers2763
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)30,9032
Polymers30,8111
Non-polymers921
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)31,1795
Polymers30,8111
Non-polymers3684
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)31,4568
Polymers30,8111
Non-polymers6457
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)30,9953
Polymers30,8111
Non-polymers1842
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)31,1795
Polymers30,8111
Non-polymers3684
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)31,1795
Polymers30,8111
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.993, 151.860, 166.785
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: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.18 M tri-ammonium citrate, 18% v/v PEG 3350, 0.01 M Cobalt (II) chloride hexahydrate

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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: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 233281 / % possible obs: 99.3 % / Redundancy: 10.1 % / CC1/2: 0.997 / Rrim(I) all: 0.252 / Net I/σ(I): 8.49
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 36696 / CC1/2: 0.467 / Rrim(I) all: 0.252 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→48.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.16
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.264 11663 5 %
Rwork0.222 --
obs-233255 99.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.098 Å20 Å20 Å2
2---1.549 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20388 0 198 1140 21726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01321241
X-RAY DIFFRACTIONr_bond_other_d0.0350.01718932
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.63628821
X-RAY DIFFRACTIONr_angle_other_deg2.3571.57744119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98552477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26422.7251101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.843153551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.04515100
X-RAY DIFFRACTIONr_chiral_restr0.0930.22591
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0223336
X-RAY DIFFRACTIONr_gen_planes_other0.0170.024518
X-RAY DIFFRACTIONr_nbd_refined0.2150.24721
X-RAY DIFFRACTIONr_nbd_other0.2490.2126
X-RAY DIFFRACTIONr_nbtor_refined0.1760.29894
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21226
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_it1.2173.69938
X-RAY DIFFRACTIONr_mcbond_other1.2173.69937
X-RAY DIFFRACTIONr_mcangle_it1.9655.39312405
X-RAY DIFFRACTIONr_mcangle_other1.9655.39312406
X-RAY DIFFRACTIONr_scbond_it1.4633.73111303
X-RAY DIFFRACTIONr_scbond_other1.4633.73111304
X-RAY DIFFRACTIONr_scangle_it2.3715.52616416
X-RAY DIFFRACTIONr_scangle_other2.3715.52616417
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

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.9490.4218280.4161573096.2674
1.949-2.0030.4058300.3831577598.6279
2.003-2.0610.3618060.3471531598.8715
2.061-2.1240.3537860.3251492899.0233
2.124-2.1940.3327650.2991453199.2087
2.194-2.2710.2987400.2751406599.3224
2.271-2.3560.3047160.2621361599.6177
2.356-2.4530.2846930.2441316499.6835
2.453-2.5620.2916650.2411262599.8497
2.562-2.6870.2626340.2161204799.874
2.687-2.8320.2886070.2111154099.9177
2.832-3.0040.2615740.2111090199.939
3.004-3.2110.2695400.2041026699.8798
3.211-3.4680.2565040.199958199.9405
3.468-3.7980.2194660.186884299.882
3.798-4.2460.2284210.173801299.9644
4.246-4.9020.1853750.152712699.9867
4.902-6.0010.2273190.174605099.9529
6.001-8.4740.2322500.178475999.9401
8.4740.1971440.184272098.9634

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