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- PDB-2xom: Atomic resolution structure of TmCBM61 in complex with beta-1,4- ... -

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Basic information

Entry
Database: PDB / ID: 2xom
TitleAtomic resolution structure of TmCBM61 in complex with beta-1,4- galactotriose
ComponentsARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE
KeywordsHYDROLASE / GALACTAN / CARBOHYDRATE-BINDING MODULE / GLYCOSIDE HYDROLASE / BETA-SANDWICH.
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Galactose-binding domain-like / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4beta-beta-galactotriose / Arabinogalactan endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.95 Å
AuthorsCid, M. / Lodberg-Pedersen, H. / Kaneko, S. / Coutinho, P.M. / Henrissat, B. / Willats, W.G.T. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Recognition of the Helical Structure of Beta-1,4-Galactan by a New Family of Carbohydrate-Binding Modules.
Authors: Cid, M. / Pedersen, H.L. / Kaneko, S. / Coutinho, P.M. / Henrissat, B. / Willats, W.G.T. / Boraston, A.B.
History
DepositionAug 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_conn_angle / 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_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7633
Polymers17,2181
Non-polymers5452
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.915, 31.920, 67.790
Angle α, β, γ (deg.)90.00, 128.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE


Mass: 17218.098 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULES, RESIDUES 461-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MS8B / Plasmid: PCBM61 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X0S8
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose / 4beta-beta-galactotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-galactotriose
DescriptorTypeProgram
DGalpb1-4DGalpb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-Galp]{}}}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.: 284 / 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: 2.04 Å3/Da / Density % sol: 39.85 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 0.95→20 Å / Num. obs: 77217 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 0.95→1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 68.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: NONE

Resolution: 0.95→17.74 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.331 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1197 4089 5 %RANDOM
Rwork0.10381 ---
obs0.10458 77217 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.04 Å2
2---0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 0.95→17.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 35 284 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221387
X-RAY DIFFRACTIONr_bond_other_d0.0020.02974
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9741917
X-RAY DIFFRACTIONr_angle_other_deg1.05732382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51424.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.564159
X-RAY DIFFRACTIONr_chiral_restr0.1280.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.651.5783
X-RAY DIFFRACTIONr_mcbond_other0.8161.5322
X-RAY DIFFRACTIONr_mcangle_it2.51421289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9423604
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9954.5605
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.36332361
X-RAY DIFFRACTIONr_sphericity_free10.3613286
X-RAY DIFFRACTIONr_sphericity_bonded4.40932303
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 222 -
Rwork0.213 3524 -
obs--58 %

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