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- PDB-2bod: Catalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fu... -

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Basic information

Entry
Database: PDB / ID: 2bod
TitleCatalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fusca in complex with methyl cellobiosyl-4-thio-beta-cellobioside
ComponentsENDOGLUCANASE E-2
KeywordsHYDROLASE / ENDOGLUCANASE / THERMOBIFIDA FUSCA / TIM A/B FOLD / GLYCOSIDE HYDROLASE FAMILY 6 / METHYL CELLOBIOSYL-4-THIO-BETA-CELLOBIOSIDE / CARBOHYDRATE METABOLISM / CELLULOSE DEGRADATION / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide binding / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / Cellulose binding domain ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMOMONOSPORA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLarsson, A.M. / Bergfors, T. / Dultz, E. / Irwin, D.C. / Roos, A. / Driguez, H. / Wilson, D.B. / Jones, T.A.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Thermobifida Fusca Endoglucanase Cel6A in Complex with Substrate and Inhibitor: The Role of Tyrosine Y73 in Substrate Ring Distortion.
Authors: Larsson, A.M. / Bergfors, T. / Dultz, E. / Irwin, D.C. / Roos, A. / Driguez, H. / Wilson, D.B. / Jones, T.A.
History
DepositionApr 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.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
Revision 2.2Oct 16, 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

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Assembly

Deposited unit
X: ENDOGLUCANASE E-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1332
Polymers30,4371
Non-polymers6971
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.317, 66.815, 81.187
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 E-2 / ENDO-1 / 4-BETA-GLUCANASE E-2 / CELLULASE E-2 / CELLULASE E2


Mass: 30436.793 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOMONOSPORA FUSCA (bacteria) / Plasmid: POS12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26222, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1*S*_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC
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 Å3/Da / Density % sol: 36.7 %
Crystal growDetails: 20-30% POLYETHYLENGLYCOL 4000 AND 0.15-0.34 M SODIUM MALONATE, PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.134
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2002 / Details: SI MIRROR COATED WITH PLATINUM
RadiationMonochromator: ASYMMETRICALLY CUT SINGLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.134 Å / Relative weight: 1
ReflectionResolution: 1.5→18.4 Å / Num. obs: 38138 / % possible obs: 99.3 % / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.115 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.263 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TML

1tml


Resolution: 1.5→18.38 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.508 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1909 5 %RANDOM
Rwork0.185 ---
obs0.186 36229 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 46 225 2365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212297
X-RAY DIFFRACTIONr_bond_other_d0.0020.021983
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9413152
X-RAY DIFFRACTIONr_angle_other_deg0.87234620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022642
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
X-RAY DIFFRACTIONr_nbd_refined0.2090.2498
X-RAY DIFFRACTIONr_nbd_other0.2460.22354
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.21254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.51452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25322334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9023845
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1524.5818
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 122
Rwork0.249 2572

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