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- PDB-6xqf: Crystal structure of SCLam E144S mutant, a non-specific endo-beta... -

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Entry
Database: PDB / ID: 6xqf
TitleCrystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site
ComponentsGH16 family protein
KeywordsHYDROLASE / glycoside hydrolase / transglycosylation / endo-1 / 3(4)-beta-glucanases / metagenome
Function / homologyglucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / metal ion binding / GH16 family protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsLiberato, M.V. / Squina, F.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/50590-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)310177/2011-1 Brazil
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds.
Authors: Liberato, M.V. / Teixeira Prates, E. / Goncalves, T.A. / Bernardes, A. / Vilela, N. / Fattori, J. / Ematsu, G.C. / Chinaglia, M. / Machi Gomes, E.R. / Migliorini Figueira, A.C. / Damasio, A. ...Authors: Liberato, M.V. / Teixeira Prates, E. / Goncalves, T.A. / Bernardes, A. / Vilela, N. / Fattori, J. / Ematsu, G.C. / Chinaglia, M. / Machi Gomes, E.R. / Migliorini Figueira, A.C. / Damasio, A. / Polikarpov, I. / Skaf, M.S. / Squina, F.M.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH16 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8333
Polymers30,2891
Non-polymers5452
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.692, 49.868, 114.474
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 GH16 family protein


Mass: 30288.746 Da / Num. of mol.: 1 / Mutation: E144S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: sclam / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B5H9B3, glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG4000, 0.2 M magnesium chloride, and 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4583 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4583 Å / Relative weight: 1
ReflectionResolution: 1.58→45.72 Å / Num. obs: 30357 / % possible obs: 97.2 % / Redundancy: 5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Rrim(I) all: 0.094 / Net I/σ(I): 13.9 / Num. measured all: 151100 / Scaling rejects: 832
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.58-1.612.90.367335611620.6310.2470.4472.477.7
8.65-45.724.40.0529992290.9820.0270.05826.397.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.58 Å45.72 Å
Translation1.58 Å45.72 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.7data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XOF

6xof


Resolution: 1.58→45.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1899 / WRfactor Rwork: 0.1619 / FOM work R set: 0.8378 / SU B: 4.956 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1034 / SU Rfree: 0.1012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1487 5 %RANDOM
Rwork0.1714 ---
obs0.1733 28544 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.99 Å2 / Biso mean: 10.568 Å2 / Biso min: 2.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 1.58→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 35 455 2513
Biso mean--9.46 21.88 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171827
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.6652921
X-RAY DIFFRACTIONr_angle_other_deg1.5541.5984246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0935263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91322.857112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 86 -
Rwork0.285 1858 -
all-1944 -
obs--85.53 %
Refinement TLS params.Method: refined / Origin x: -8.46 Å / Origin y: -4.624 Å / Origin z: 12.934 Å
111213212223313233
T0.0232 Å2-0.0078 Å2-0.0018 Å2-0.0286 Å2-0.0059 Å2--0.0032 Å2
L1.0062 °2-0.1681 °20.2056 °2-1.0288 °2-0.3185 °2--0.765 °2
S0.0075 Å °-0.0323 Å °-0.0262 Å °0.0406 Å °0.0046 Å °0.0073 Å °0.002 Å °-0.0317 Å °-0.0121 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 265
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION1A401 - 855

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