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- PDB-6xof: Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-gluca... -

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Basic information

Entry
Database: PDB / ID: 6xof
TitleCrystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16
ComponentsGH16 family protein
KeywordsHYDROLASE / metagenomics / beta-glucan / endo-1 / 3(4)-beta-glucanases
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLiberato, M.V. / Bernardes, A. / Polikarpov, I. / 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 7, 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

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Assembly

Deposited unit
A: GH16 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4633
Polymers30,3311
Non-polymers1322
Water8,431468
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)42.855, 46.673, 115.055
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: 30330.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Metagenomics
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: sclam / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A0B5H9B3, glucan endo-1,3-beta-D-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→46.67 Å / Num. obs: 37616 / % possible obs: 99.4 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Rrim(I) all: 0.062 / Net I/σ(I): 10.6 / Num. measured all: 70423
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
1.5-1.531.80.398328417880.7330.3980.5631.497.2
8.22-46.671.50.0134412890.9990.0130.01924.199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å43.25 Å
Translation1.5 Å43.25 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
APEX 2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 1.5→43.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1591 / WRfactor Rwork: 0.1348 / FOM work R set: 0.8827 / SU B: 2.64 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0716 / SU Rfree: 0.0698 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 1815 4.8 %RANDOM
Rwork0.1452 ---
obs0.1463 35738 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.75 Å2 / Biso mean: 9.543 Å2 / Biso min: 2.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2---0.16 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.5→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 19 468 2587
Biso mean--5 23.43 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181988
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.6453038
X-RAY DIFFRACTIONr_angle_other_deg1.551.5834592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7775280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16322.857119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53515347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1021511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 125 -
Rwork0.261 2555 -
all-2680 -
obs--97.07 %
Refinement TLS params.Method: refined / Origin x: 5.1013 Å / Origin y: 3.6928 Å / Origin z: 15.216 Å
111213212223313233
T0.0068 Å20.0027 Å20.0007 Å2-0.0024 Å20.0008 Å2--0.0096 Å2
L0.0733 °20.0981 °2-0.0341 °2-0.1477 °2-0.0596 °2--0.1774 °2
S0.0015 Å °-0.003 Å °-0.0001 Å °0.0034 Å °-0.0042 Å °0.0115 Å °0.0065 Å °0.0174 Å °0.0027 Å °

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