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- PDB-1uxx: CBM6ct from Clostridium thermocellum in complex with xylopentaose -

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Basic information

Entry
Database: PDB / ID: 1uxx
TitleCBM6ct from Clostridium thermocellum in complex with xylopentaose
ComponentsXYLANASE U
KeywordsCARBOHYDRATE BINDING MODULE / CBM6 / XYLOPENTAOSE BINDING / XYLAN DEGRADATION
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 ...NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase family 11/12 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCzjzek, M. / Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Henrissat, D.B.B. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Crystal Structure of the Family 6 Carbohydrate Binding Module from Cellvibrio Mixtus Endoglucanase 5A in Complex with Oligosaccharides Reveals Two Distinct Binding Sites with Different Ligand Specificities
Authors: Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Bolam, D. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Henrissat, B. / Planas, A. / Gilbert, H.J. / Czjzek, M.
History
DepositionMar 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.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 / _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_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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: XYLANASE U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8343
Polymers14,1151
Non-polymers7192
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)27.480, 51.680, 36.130
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein XYLANASE U / ENDO-1 / 4-BETA-XYLANASE


Mass: 14115.347 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 248-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O52780, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a212h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. A MEMBER OF THE XYLAN ...CATALYSES THE ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. A MEMBER OF THE XYLAN DEGRADATION PATHWAY.
Sequence detailsCBM6 IS A FRAGMENT OF THIS SEQUENCE

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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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 4.6
Details: 20% PEG 1000, 0.2 M SODIUM ACETATE, 0.1 M ACETATE BUFFER PH4.6, pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
212 %(w/v)PEG60001reservoir
32.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→52 Å / Num. obs: 13033 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 9.1 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 9.1

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Processing

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

1gmm


Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.71 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 640 4.9 %RANDOM
Rwork0.18 ---
obs0.182 12391 99.4 %-
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: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.14 Å2
2--0.23 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 47 108 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021998
X-RAY DIFFRACTIONr_bond_other_d0.0020.02830
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9941360
X-RAY DIFFRACTIONr_angle_other_deg0.8331936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125123
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_restr0.0950.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02189
X-RAY DIFFRACTIONr_nbd_refined0.2370.2141
X-RAY DIFFRACTIONr_nbd_other0.2560.2939
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.5607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8492975
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1433391
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3554.5385
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 53
Rwork0.204 919
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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