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- PDB-2vi0: Lichenase CtLic26 in complex with a thio-oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 2vi0
TitleLichenase CtLic26 in complex with a thio-oligosaccharide
ComponentsEndoglucanase H
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / GLYCOSIDASE / CELLULOSE DEGRADATION / ENZYME GLYCOSIDE HYDROLASE LICHENASE BETA GLUCANASE GH26 G
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain ...Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Endoglucanase H
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsMoney, V.A. / Ducros, V.M. / Davies, G.J.
Citation
Journal: Org. Biomol. Chem. / Year: 2008
Title: Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants.
Authors: Money, V.A. / Cartmell, A. / Guerreiro, C.I. / Ducros, V.M. / Fontes, C.M. / Gilbert, H.J. / Davies, G.J.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides: Structure and Activity of a Clostridium Thermocellum Lichenase, Ctlic26A.
Authors: Taylor, E.J. / Goyal, A. / Guerreiro, C.I.P.D. / Prates, J.A.M. / Money, V.A. / Ferry, N. / Morland, C. / Planas, A. / Macdonald, J.A. / Stick, R.V. / Gilbert, H.J. / Fontes, C.M.G.A. / Davies, G.J.
#2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases.
Authors: Money, V.A. / Smith, N.L. / Scaffidi, A. / Stick, R.V. / Gilbert, H.J. / Davies, G.J.
History
DepositionNov 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_assembly_gen / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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: Endoglucanase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7603
Polymers32,0451
Non-polymers7152
Water6,846380
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.578, 62.648, 79.067
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 Endoglucanase H / Cellulase H / Endo-1 / 4-beta-glucanase H / EgH


Mass: 32045.432 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-304 / Mutation: G271E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: celH, Cthe_1472 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P16218, cellulase
#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: Polysaccharide 4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 372.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5_4*S]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 293 TO GLY
Nonpolymer detailsMETHYL O-BETA-D-GLUCOPYRANOSYL- (1,4)-O-BETA-D-GLUCOPYRAN OSYL)- (1,3)-S-BETA-D-GLUCOPYRANOSYL- ( ...METHYL O-BETA-D-GLUCOPYRANOSYL- (1,4)-O-BETA-D-GLUCOPYRAN OSYL)- (1,3)-S-BETA-D-GLUCOPYRANOSYL- ( 1,4)-O- (4-THIO-BETA- D-GLUCOPYRANOSYL)-(1, 4)-BETA-D-GLUCOPYRANOSIDE (VAM): THIS IS THE REDUCING TERMINAL DISACCHARIDE OF A THIO-PENTASACCHARIDE LIGAND. COUMPOUND 2A FROM MOREAU ET AL 1996 BIOORG MED CHEM, 4, 1849-1855 GLUCOSE (GLC): THESE TWO GLUCOSE MOIETIES ARE THE NON REDUCING TERMINAL DISACCHARIDE OF A THIO-PENTASACCHARIDE LIGAND. COUMPOUND 2A FROM MOREAU ET AL 1996 BIOORG MED CHEM, 4, 1849-1855

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.5
Details: 0.15 M AMMONIUM SULPHATE, 30 % PEG 5K, MME, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.51→34.88 Å / Num. obs: 3620 / % possible obs: 95.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 72

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BV9

2bv9


Resolution: 1.51→34.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.274 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1905 5 %RANDOM
Rwork0.153 ---
obs0.154 36205 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.51→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 47 380 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222482
X-RAY DIFFRACTIONr_bond_other_d0.0020.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9163419
X-RAY DIFFRACTIONr_angle_other_deg1.14333940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48723.937127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9791.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46822339
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1931040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0864.51069
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 97
Rwork0.231 1808

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