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- PDB-6ub2: Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanas... -

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Basic information

Entry
Database: PDB / ID: 6ub2
TitleCrystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV)
ComponentsEndo-beta-1,3-glucanase
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 / Endo-beta-1,3-glucanase
Function and homology information
Biological speciesLentinula edodes (shiitake mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSantos, C.R. / Lima, E.A. / Mandelli, F. / Vieira, P.S. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,3-glucanase
B: Endo-beta-1,3-glucanase
C: Endo-beta-1,3-glucanase
D: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,33415
Polymers115,1234
Non-polymers1,21111
Water22,8971271
1
A: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0123
Polymers28,7811
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1084
Polymers28,7811
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0123
Polymers28,7811
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2045
Polymers28,7811
Non-polymers4234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.817, 75.159, 99.450
Angle α, β, γ (deg.)90.000, 103.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endo-beta-1,3-glucanase


Mass: 28780.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinula edodes (shiitake mushroom) / Gene: glu1 / Production host: Escherichia coli (E. coli) / References: UniProt: G9M5R4
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1271 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M ammonium sulfate 0.1 M MES 0% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→49.09 Å / Num. obs: 94945 / % possible obs: 98.2 % / Redundancy: 6.9 % / CC1/2: 0.996 / Net I/σ(I): 9.05
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 15156 / CC1/2: 0.628

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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→49.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 4748 5 %RANDOM
Rwork0.1724 ---
obs0.1744 90200 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.93 Å2 / Biso mean: 22.488 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å2-0.24 Å2
2--2.97 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.8→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 67 1271 8814
Biso mean--52.39 34.54 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0127795
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176646
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.63210707
X-RAY DIFFRACTIONr_angle_other_deg2.4531.55515490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4795993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86924.715333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.441151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.529158
X-RAY DIFFRACTIONr_chiral_restr0.0850.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028921
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021643
X-RAY DIFFRACTIONr_mcbond_it1.1372.2873972
X-RAY DIFFRACTIONr_mcbond_other1.1372.2873971
X-RAY DIFFRACTIONr_mcangle_it1.7213.4264959
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 341 -
Rwork0.351 6467 -
all-6808 -
obs--96.29 %

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