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- PDB-6ub7: Crystal structure of a GH128 (subgroup V) exo-beta-1,3-glucanase ... -

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Basic information

Entry
Database: PDB / ID: 6ub7
TitleCrystal structure of a GH128 (subgroup V) exo-beta-1,3-glucanase from Cryptococcus neoformans (CnGH128_V)
ComponentsGlyco_hydro_cc domain-containing protein
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homology: / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / : / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSantos, C.R. / Costa, P.A.C.R. / 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

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Assembly

Deposited unit
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8132
Polymers32,7741
Non-polymers391
Water2,468137
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)58.896, 60.066, 96.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 32774.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli (E. coli) / References: UniProt: J9VQQ4
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: sodium/potassium phosphate 2.4 M 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.8→48.02 Å / Num. obs: 31515 / % possible obs: 98 % / Redundancy: 4.56 % / CC1/2: 0.999 / Net I/σ(I): 13.47
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 4570 / CC1/2: 0.691

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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: 1.8→28.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1593 5 %RANDOM
Rwork0.1849 ---
obs0.1865 30032 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.91 Å2 / Biso mean: 32.528 Å2 / Biso min: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.8→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 1 137 2206
Biso mean--34.41 41.45 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132145
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171815
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.6362932
X-RAY DIFFRACTIONr_angle_other_deg2.3981.5724246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6275252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27924.786117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31115325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.112154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022417
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02447
X-RAY DIFFRACTIONr_mcbond_it2.1343.3371014
X-RAY DIFFRACTIONr_mcbond_other2.1213.3361013
X-RAY DIFFRACTIONr_mcangle_it3.1694.9891264
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 109 -
Rwork0.352 1892 -
all-2001 -
obs--85.04 %

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