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- PDB-5mwk: Glycoside hydrolase BT_0986 -

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Basic information

Entry
Database: PDB / ID: 5mwk
TitleGlycoside hydrolase BT_0986
ComponentsGlycoside hydrolase family 2, sugar binding protein
KeywordsHYDROLASE / glycoside hydrolase / rhamnosidase / plant pectin / CAZy family 106
Function / homologyalpha-L-rhamnosidase / Glycosyl hydrolase 2 galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / metal ion binding / BROMIDE ION / IODIDE ION / Glycoside hydrolase family 2, sugar binding protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
CitationJournal: Nature / Year: 2017
Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.
Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_validate_close_contact / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_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_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 2, sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4316
Polymers125,1351
Non-polymers1,2965
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint4 kcal/mol
Surface area40450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.254, 86.216, 123.200
Angle α, β, γ (deg.)90.00, 99.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycoside hydrolase family 2, sugar binding protein


Mass: 125134.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A931
#2: Polysaccharide alpha-L-rhamnopyranose-(1-2)-alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl- ...alpha-L-rhamnopyranose-(1-2)-alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose-(1-2)]beta-D-galactopyranose-(1-2)-alpha-D-aceric acid-(1-3)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 968.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][a-L-Rhap]{[(3+1)][a-D-5-deoxy-Xylf]{[(2+1)][b-D-Galp]{[(2+1)][a-L-Fucp2Me]{}[(4+1)][a-L-Arap]{[(2+1)][a-L-Rhap]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 405 molecules

#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 550 MME, 15% (w/v) 20000, 50 mM Imidazol, 50 mM MES pH 6.5, 30 mM NaF, 30 mM NaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2→45.4 Å / Num. obs: 90046 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Num. unique obs: 4436 / CC1/2: 0.512 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQM

5mqm


Resolution: 2→45.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.825 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 4464 5 %RANDOM
Rwork0.19945 ---
obs0.20143 85551 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.896 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.29 Å2
2--0.26 Å20 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 2→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8291 0 67 401 8759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198580
X-RAY DIFFRACTIONr_bond_other_d0.0010.027838
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.95611634
X-RAY DIFFRACTIONr_angle_other_deg0.965318212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61651039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82524.089406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.646151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4431557
X-RAY DIFFRACTIONr_chiral_restr0.090.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021768
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_it1.8242.9874159
X-RAY DIFFRACTIONr_mcbond_other1.8222.9864158
X-RAY DIFFRACTIONr_mcangle_it2.7694.4655194
X-RAY DIFFRACTIONr_mcangle_other2.7694.4665195
X-RAY DIFFRACTIONr_scbond_it2.1323.2284421
X-RAY DIFFRACTIONr_scbond_other2.1313.2284422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3994.7376440
X-RAY DIFFRACTIONr_long_range_B_refined4.59733.0749000
X-RAY DIFFRACTIONr_long_range_B_other4.58733.0338947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 296 -
Rwork0.313 6308 -
obs--98.38 %

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