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- PDB-3o5s: Crystal Structure of the endo-beta-1,3-1,4 glucanase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 3o5s
TitleCrystal Structure of the endo-beta-1,3-1,4 glucanase from Bacillus subtilis (strain 168)
ComponentsBeta-glucanase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / BETA-JELLY ROLL
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process / extracellular region
Similarity search - Function
Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSantos, C.R. / Tonoli, C.C.C. / Souza, A.R. / Furtado, G.P. / Ribeiro, L.F. / Ward, R.J. / Murakami, M.T.
CitationJournal: PROCESS BIOCHEM / Year: 2011
Title: Biochemical and structural characterization of a Beta-1,3 1,4-glucanase from Bacillus subtilis 168
Authors: Furtado, G.P. / Ribeiro, L.F. / Santos, C.R. / Tonoli, C.C. / De Souza, A.R. / Oliveira, R.R. / Tyago, M.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1943
Polymers26,8721
Non-polymers3222
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.758, 103.758, 102.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beta-glucanase / Endo-beta-1 / 3-1 / 4 glucanase / 1 / 3-1 / 4-beta-D-glucan 4-glucanohydrolase / Lichenase


Mass: 26871.650 Da / Num. of mol.: 1 / Fragment: UNP residues 26-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: bglS, bgl, licS, BSU39070, N15B / Production host: Escherichia coli (E. coli) / References: UniProt: P04957, licheninase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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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, sitting drop / pH: 7
Details: lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: Si 111 double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.2→29.8 Å / Num. all: 27791 / Num. obs: 27587 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.4 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.8 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.252 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29196 1407 5.1 %RANDOM
Rwork0.24943 ---
obs0.25156 26383 96.08 %-
all-27575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 20 153 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221782
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9162425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98824.50591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.82155
X-RAY DIFFRACTIONr_chiral_restr0.1570.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211413
X-RAY DIFFRACTIONr_mcbond_it0.9741.51051
X-RAY DIFFRACTIONr_mcangle_it1.59821686
X-RAY DIFFRACTIONr_scbond_it2.883731
X-RAY DIFFRACTIONr_scangle_it4.0614.5739
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 89 -
Rwork0.271 1776 -
obs--88.73 %
Refinement TLS params.Method: refined / Origin x: -35.4498 Å / Origin y: 8.9872 Å / Origin z: 20.2148 Å
111213212223313233
T0.0727 Å2-0.0175 Å2-0.0093 Å2-0.0291 Å2-0.0119 Å2--0.0377 Å2
L3.0611 °20.5107 °20.8457 °2-1.8845 °2-0.3883 °2--2.2539 °2
S-0.0657 Å °0.1817 Å °-0.3089 Å °-0.2751 Å °0.109 Å °0.0002 Å °0.0921 Å °0.1666 Å °-0.0433 Å °

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