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- PDB-2wao: Structure of a family two carbohydrate esterase from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 2wao
TitleStructure of a family two carbohydrate esterase from Clostridium thermocellum in complex with cellohexaose
ComponentsENDOGLUCANASE E
KeywordsHYDROLASE / PLANT CELL WALL DEGRADATION / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / ESTERASE / CELLULASES / GLYCOSIDASE / CARBOHYDRATE BINDING / CELLULOSE DEGRADATION
Function / homology
Function and homology information


glucomannan catabolic process / acetylxylan esterase / acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cellulose binding / cellulase / cellulase activity / xylan catabolic process / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / : / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / Glycoside hydrolase, family 5, conserved site ...Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / : / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / 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 domain-like / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-cellopentaose / FORMIC ACID / Cellulase/esterase CelE
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMontainer, C. / Money, V.A. / Pires, V.M.R. / Flint, J.E. / Pinheiro, B.A. / Goyal, A. / Prates, J.A.M. / Izumi, A. / Stalbrand, H. / Kolenova, K. ...Montainer, C. / Money, V.A. / Pires, V.M.R. / Flint, J.E. / Pinheiro, B.A. / Goyal, A. / Prates, J.A.M. / Izumi, A. / Stalbrand, H. / Kolenova, K. / Topakas, E. / Dodson, E.J. / Bolam, D.N. / Davies, G.J. / Fontes, C.M.G.A. / Gilbert, H.J.
CitationJournal: Plos Biol. / Year: 2009
Title: The Active Site of a Carbohydrate Esterase Displays Divergent Catalytic and Noncatalytic Binding Functions.
Authors: Montanier, C. / Money, V.A. / Pires, V.M.R. / Flint, J.E. / Pinheiro, B.A. / Goyal, A. / Prates, J.A.M. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. ...Authors: Montanier, C. / Money, V.A. / Pires, V.M.R. / Flint, J.E. / Pinheiro, B.A. / Goyal, A. / Prates, J.A.M. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / Dodson, E.J. / Bolam, D.N. / Davies, G.J. / Fontes, C.M.G.A. / Gilbert, H.J.
History
DepositionFeb 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
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 / 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 / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,03413
Polymers37,6991
Non-polymers1,33512
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.634, 60.082, 69.000
Angle α, β, γ (deg.)90.00, 78.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE E / ACETYL ESTERASE / ENDO-1 / 4-BETA-GLUCANASE E / CELLULASE E / EGE


Mass: 37699.105 Da / Num. of mol.: 1
Fragment: C TERMINAL DOMAIN OF CEL5C-CES2A, RESIDUES 485-814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10477, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.32 Å3/Da / Density % sol: 46.93 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Type: ESRF / Wavelength: 0.9757
DetectorDetector: CCD / Date: Dec 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 1.8→67.6 Å / Num. obs: 31011 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.9 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.29 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1550 5 %RANDOM
Rwork0.144 ---
obs0.146 29236 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 89 430 3041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9683706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16224.153118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34415417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022065
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21275
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21853
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1051.51710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56722657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.79631183
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9974.51039
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 97
Rwork0.191 2118

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