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- PDB-5e7g: Crystal structure of Bacova_02650 with xylogluco-oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 5e7g
TitleCrystal structure of Bacova_02650 with xylogluco-oligosaccharide
ComponentsIPT/TIG domain-containing protein BACOVA_02650
KeywordsSUGAR BINDING PROTEIN / carbohydrate-binding protein
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan catabolic process / polysaccharide binding / cell outer membrane
Similarity search - Function
Surface glycan-binding protein B, xyloglucan binding domain / Surface glycan-binding protein B xyloglucan binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
IPT/TIG domain-containing protein BACOVA_02650
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
Model detailsSusD homolog
AuthorsKoropatkin, N.M.
CitationJournal: Mbio / Year: 2016
Title: Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont.
Authors: Tauzin, A.S. / Kwiatkowski, K.J. / Orlovsky, N.I. / Smith, C.J. / Creagh, A.L. / Haynes, C.A. / Wawrzak, Z. / Brumer, H. / Koropatkin, N.M.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: 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_struct_oper_list / pdbx_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_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.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 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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: IPT/TIG domain-containing protein BACOVA_02650
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,64910
Polymers49,6511
Non-polymers1,9989
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-20 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.390, 207.390, 117.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein IPT/TIG domain-containing protein BACOVA_02650


Mass: 49651.199 Da / Num. of mol.: 1 / Fragment: UNP residues 34-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02650 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: A7LXT4
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1387.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,9,8/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-1-1-2-2-2/a4-b1_b4-c1_b6-i1_c4-d1_c6-h1_d4-e1_d6-g1_e4-f1WURCSPDB2Glycan 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]{[(4+1)][b-D-Glcp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 134 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 4.91 Å3/Da / Density % sol: 74.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.1 to 1.5 M ammonium sulphate, 30 to 70 mM sodium cacodylate pH 6.5. To decrease crystal nucleation, 0.3 ml of paraffin oil was overlaid on top of 0.5 mls of mother liquor
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.37→39.19 Å / Num. obs: 39362 / % possible obs: 99.9 % / Redundancy: 8.2 % / Net I/σ(I): 20.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.37→39.19 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1885 5.09 %
Rwork0.1975 72811 -
obs0.199 39362 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.97 Å2 / Biso mean: 57.81 Å2 / Biso min: 31.53 Å2
Refinement stepCycle: final / Resolution: 2.37→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 231 126 3782
Biso mean--76.5 47.61 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053637
X-RAY DIFFRACTIONf_angle_d0.9054976
X-RAY DIFFRACTIONf_chiral_restr0.033602
X-RAY DIFFRACTIONf_plane_restr0.003622
X-RAY DIFFRACTIONf_dihedral_angle_d13.2021241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.39890.31471260.30482613X-RAY DIFFRACTION100
2.3989-2.42930.31041570.30642552X-RAY DIFFRACTION100
2.4293-2.46120.36351180.29762625X-RAY DIFFRACTION100
2.4612-2.4950.29241390.26512609X-RAY DIFFRACTION100
2.495-2.53060.31181270.28812625X-RAY DIFFRACTION100
2.5306-2.56840.31641450.27112617X-RAY DIFFRACTION100
2.5684-2.60850.32131610.26012543X-RAY DIFFRACTION100
2.6085-2.65120.25141310.2452612X-RAY DIFFRACTION100
2.6512-2.69690.33591310.25962620X-RAY DIFFRACTION100
2.6969-2.7460.29851610.25512559X-RAY DIFFRACTION100
2.746-2.79880.28411250.25522624X-RAY DIFFRACTION100
2.7988-2.85590.30161230.25512618X-RAY DIFFRACTION100
2.8559-2.9180.30271280.24922617X-RAY DIFFRACTION100
2.918-2.98580.31351390.24422590X-RAY DIFFRACTION100
2.9858-3.06050.27441300.24232610X-RAY DIFFRACTION100
3.0605-3.14320.25111510.24752599X-RAY DIFFRACTION100
3.1432-3.23560.33961290.22332623X-RAY DIFFRACTION100
3.2356-3.340.26491410.22722591X-RAY DIFFRACTION100
3.34-3.45930.27471390.21962594X-RAY DIFFRACTION100
3.4593-3.59770.23261420.20692604X-RAY DIFFRACTION100
3.5977-3.76130.22641480.19142577X-RAY DIFFRACTION100
3.7613-3.95950.20811520.17222600X-RAY DIFFRACTION100
3.9595-4.20730.17971180.15672628X-RAY DIFFRACTION100
4.2073-4.53170.15991570.132578X-RAY DIFFRACTION100
4.5317-4.98690.13281410.13062602X-RAY DIFFRACTION100
4.9869-5.70660.1421500.14142596X-RAY DIFFRACTION100
5.7066-7.18250.17981550.16722591X-RAY DIFFRACTION100
7.1825-39.190.21241420.16442594X-RAY DIFFRACTION99

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