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- PDB-2bv9: HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFE... -

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Basic information

Entry
Database: PDB / ID: 2bv9
TitleHOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CtLIC26A
ComponentsENDOGLUCANASE H
KeywordsHYDROLASE / BETA-1 4 BETA-1 3 GLUCANASE / GLYCOSIDE HYDROLASE FAMILY 26
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / cellulase 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
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsTaylor, 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. ...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.
CitationJournal: 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.
History
DepositionJun 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE H


Theoretical massNumber of molelcules
Total (without water)33,1891
Polymers33,1891
Non-polymers00
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.828, 63.646, 100.021
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 / CELLULOSE BINDING PROTEIN A / EGH / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE H / LICH26A


Mass: 33188.633 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: F1/YS / Plasmid: PCF2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16218, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE ...HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CTLIC26A RESIDUES 1-3 (MAS) OF THE GIVEN SEQUENCE ARE DERIVED FROM THE CLONING VECTOR PET 21A AND ARE 282-290 (LEHHHHHH).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growDetails: 0.3-1.2M NA FORMATE, 0.1M NA CACODYLATE BUFFERED AT PH 6.5 AND 5-20% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2003 / Details: RADII TOROIDAL MIRROR
RadiationMonochromator: GE(220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→36 Å / Num. obs: 51705 / % possible obs: 96.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 14.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→36.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.853 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 2547 5.1 %RANDOM
Rwork0.131 ---
obs0.132 47084 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 465 2772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212417
X-RAY DIFFRACTIONr_bond_other_d0.0070.022027
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.8833288
X-RAY DIFFRACTIONr_angle_other_deg1.74234715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7423.769130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4011514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined0.2210.2498
X-RAY DIFFRACTIONr_nbd_other0.240.22073
X-RAY DIFFRACTIONr_nbtor_refined0.2070.21209
X-RAY DIFFRACTIONr_nbtor_other0.1470.21243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5911.51827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56522270
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48431263
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3134.51018
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
Rfree0.176 188
Rwork0.143 3336

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