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

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Entry
Database: PDB / ID: 6xql
TitleCrystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with cellohexaose, 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 / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water4,558253
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)38.400, 49.006, 113.995
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.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22.5 % 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: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.97→45.02 Å / Num. obs: 15639 / % possible obs: 98.5 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.039 / Rrim(I) all: 0.089 / Net I/σ(I): 14.2 / Num. measured all: 75680
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
1.97-2.023.20.328326710170.8960.2090.3912.892.8
9.03-45.024.80.0299732010.9990.0150.03335.296.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.13 Å45.02 Å
Translation6.13 Å45.02 Å

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Processing

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

6xof


Resolution: 1.97→45.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.72 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 774 5 %RANDOM
Rwork0.1699 ---
obs0.1733 14777 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.95 Å2 / Biso mean: 22.076 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å2-0 Å2
2--2.65 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.97→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 35 253 2306
Biso mean--22.5 32.4 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132118
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171777
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.6642890
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5964116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4225258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47622.566113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8131511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
LS refinement shellResolution: 1.97→2.021 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 62 -
Rwork0.252 1023 -
all-1085 -
obs--93.7 %
Refinement TLS params.Method: refined / Origin x: -8.634 Å / Origin y: 4.5881 Å / Origin z: -13.1801 Å
111213212223313233
T0.0603 Å20.0082 Å2-0.0023 Å2-0.0151 Å2-0.0025 Å2--0.0053 Å2
L1.5071 °20.3854 °2-0.628 °2-1.0953 °2-0.5829 °2--0.9177 °2
S0.0173 Å °-0.0815 Å °0.0816 Å °-0.0268 Å °0.0359 Å °0.0446 Å °-0.013 Å °-0.0443 Å °-0.0533 Å °

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