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

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Basic information

Entry
Database: PDB / ID: 6xqm
TitleCrystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with laminarihexaose, presenting a laminaribiose and a 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-D-glucopyranose / PHOSPHATE ION / GH16 family protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 1.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: GH16 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9465
Polymers30,2891
Non-polymers6584
Water5,206289
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)40.170, 75.610, 83.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 291 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 27.5 % PEG4000, 0.2 M magnesium chloride, and 0.1 M MES

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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: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.85→41.74 Å / Num. obs: 22433 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.052 / Rrim(I) all: 0.179 / Net I/σ(I): 8.1 / Num. measured all: 255230 / Scaling rejects: 11353
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
1.85-1.899.61.361302613570.7810.4531.4371.399.4
9.06-41.749.50.05523122430.9990.0180.05819.399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.11 Å36.2 Å
Translation6.11 Å36.2 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XOF

6xof


Resolution: 1.85→36.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.94 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1061 4.7 %RANDOM
Rwork0.1738 ---
obs0.1759 21312 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.78 Å2 / Biso mean: 24.389 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.85→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 41 289 2396
Biso mean--23.93 38.05 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132200
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171867
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6683006
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5974341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80422.605119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815.091328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 71 -
Rwork0.327 1548 -
all-1619 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 14.394 Å / Origin y: -0.813 Å / Origin z: 92.159 Å
111213212223313233
T0.0821 Å2-0.0148 Å2-0.0132 Å2-0.007 Å2-0.0147 Å2--0.106 Å2
L1.2055 °2-0.0373 °2-0.0364 °2-1.7694 °2-0.7912 °2--2.7144 °2
S-0.066 Å °0.0417 Å °-0.0719 Å °0.046 Å °0.0471 Å °-0.1041 Å °-0.1037 Å °0.0242 Å °0.0188 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 266
2X-RAY DIFFRACTION1A301 - 305
3X-RAY DIFFRACTION1A401 - 689

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