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- PDB-1ux7: Carbohydrate-Binding Module CBM36 in complex with calcium and xyl... -

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Basic information

Entry
Database: PDB / ID: 1ux7
TitleCarbohydrate-Binding Module CBM36 in complex with calcium and xylotriose
ComponentsENDO-1,4-BETA-XYLANASE D
KeywordsCARBOHYDRATE-BINDING MODULE / CARBOHYDRATE BINDING DOMAIN / HYDROLASE / XYLAN / CALCIUM / XYLANASE GH43 / CARBOHYDRATE-BINDING MODULE CBM36
Function / homology
Function and homology information


non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like ...: / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Arabinoxylan arabinofuranohydrolase
Similarity search - Component
Biological speciesPAENIBACILLUS POLYMYXA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDavies, G.J. / Boraston, A.B. / Jamal, S.
CitationJournal: Structure / Year: 2004
Title: Ab Initio Structure Determination and Functional Characterization of Cbm36: A New Family of Calcium-Dependent Carbohydrate Binding Modules
Authors: Jamal, S. / Boraston, A.B. / Turkenburg, J.P. / Tarbouriech, N. / Ducros, V.M.-A. / Davies, G.J.
History
DepositionFeb 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: 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
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: ENDO-1,4-BETA-XYLANASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2685
Polymers12,6771
Non-polymers5914
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.581, 52.132, 54.766
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 ENDO-1,4-BETA-XYLANASE D / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE D / XYLANASE D


Mass: 12676.921 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING DOMAIN, RESIDUES 516-635
Source method: isolated from a genetically manipulated source
Details: XYLOTRIOSE CALCIUM SULFATE / Source: (gene. exp.) PAENIBACILLUS POLYMYXA (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45796
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-1)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-1DXylpbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a1-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSHOWS XYLANASE ACTIVITY, ALPHA-L- ARABINOFURANOSIDASE ACTIVITY AND ENDOHYDROLYSIS OF 1,4-BETA-D- ...SHOWS XYLANASE ACTIVITY, ALPHA-L- ARABINOFURANOSIDASE ACTIVITY AND ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. CARBOHYDRATE-BINDING MODULE CBM36. THIS DOMAIN WAS FORMALLY KNOWN AS AN X9 MODULE
Sequence detailsEXPRESSION OF C-TERMINAL CBM36 DOMAIN ONLY

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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: 38.5 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 18133 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 12 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE

Resolution: 1.5→37.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.192 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 915 5 %RANDOM
Rwork0.155 ---
obs0.157 17217 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: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---1.25 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 27 160 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021934
X-RAY DIFFRACTIONr_bond_other_d0.0020.02788
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9511272
X-RAY DIFFRACTIONr_angle_other_deg1.88231837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355118
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_restr0.0910.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021041
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02183
X-RAY DIFFRACTIONr_nbd_refined0.1960.2128
X-RAY DIFFRACTIONr_nbd_other0.2640.2923
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.2549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4130.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1521.5585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8382941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4383349
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.574.5331
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
Rfree0.205 59
Rwork0.159 1177

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