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- PDB-3axe: The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase V... -

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Basic information

Entry
Database: PDB / ID: 3axe
TitleThe truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase V18Y/W203Y in complex with cellotetraose (cellobiose density was observed)
ComponentsBeta-glucanase
KeywordsHYDROLASE / glucanase / cellobiose/cellotetraose
Function / homology
Function and homology information


licheninase / licheninase activity / carbohydrate metabolic process
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 ...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
beta-cellobiose / Beta-glucanase
Similarity search - Component
Biological speciesFibrobacter succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHuang, J.W. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Lai, H.L. / Chen, C.C. / Ma, Y. / Huang, C.H. / Zheng, Y. / Liu, J.R. / Guo, R.T.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: Rational design to improve thermostability and specific activity of the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase
Authors: Huang, J.W. / Cheng, Y.S. / Ko, T.P. / Lin, C.Y. / Lai, H.L. / Chen, C.C. / Ma, Y. / Zheng, Y. / Huang, C.H. / Zou, P. / Liu, J.R. / Guo, R.T.
History
DepositionApr 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,4527
Polymers27,8281
Non-polymers6256
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.091, 70.404, 76.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27827.656 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-271 / Mutation: V18Y, W203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fibrobacter succinogenes (bacteria) / Strain: ATCC 19169, S85 / Gene: Fisuc_2961, FSU_0226 / Plasmid: pET 32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17989, licheninase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M Tris, pH 8.5, 0.4M Calcium acetate, 33% PEG 5KMME, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→25 Å / Num. all: 33431 / Num. obs: 32609 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.7
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3199 / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
XTALVIEWrefinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZM1

1zm1


Resolution: 1.53→25 Å / σ(F): 0
RfactorNum. reflection
Rfree0.201 1584
Rwork0.182 -
all-33431
obs-31990
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 35 332 2233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection% reflection
Rfree0.281 135 -
Rwork0.238 --
obs-2771 85 %

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