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- PDB-5gub: Crystal structure of solute-binding protein complexed with sulfat... -

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Basic information

Entry
Database: PDB / ID: 5gub
TitleCrystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide
ComponentsExtracellular solute-binding protein family 1
KeywordsSUGAR BINDING PROTEIN / glycosaminoglycan / ABC transporter / solute-binding protein
Function / homology
Function and homology information


Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UNSATURATED CHONDROITIN DISACCHARIDE / Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesStreptobacillus moniliformis strain DSM 12112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsOiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aids for Scientific Research from the Japanese Society for the Promotion of Science Japan
Mizutani Foundation for Glycoscience Japan
Danone Institute of Japan Foundation Japan
CitationJournal: Sci Rep / Year: 2017
Title: A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Authors: Oiki, S. / Mikami, B. / Maruyama, Y. / Murata, K. / Hashimoto, W.
History
DepositionAug 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_unobs_or_zero_occ_atoms.label_asym_id / _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 2.1Nov 8, 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
A: Extracellular solute-binding protein family 1
B: Extracellular solute-binding protein family 1
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,82816
Polymers165,7363
Non-polymers2,09213
Water20,7531152
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9225
Polymers55,2451
Non-polymers6774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint10 kcal/mol
Surface area20270 Å2
MethodPISA
2
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0467
Polymers55,2451
Non-polymers8016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint9 kcal/mol
Surface area20310 Å2
MethodPISA
3
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8604
Polymers55,2451
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint10 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.914, 112.213, 166.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Extracellular solute-binding protein family 1


Mass: 55245.367 Da / Num. of mol.: 3 / Fragment: UNP residues 19-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptobacillus moniliformis strain DSM 12112 (bacteria)
Strain: DSM 12112 / Gene: Smon_0123 / Production host: Escherichia coli (E. coli) / References: UniProt: D1AWE0
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / UNSATURATED CHONDROITIN DISACCHARIDE


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 379.317 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with ring modification on monosaccharide components
References: UNSATURATED CHONDROITIN DISACCHARIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1162 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1152 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M MES (pH 6.0), 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 143362 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.8
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y3N

1y3n


Resolution: 1.78→41.569 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 6983 4.88 %
Rwork0.174 --
obs0.1756 143057 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→41.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11465 0 132 1152 12749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711924
X-RAY DIFFRACTIONf_angle_d1.06516156
X-RAY DIFFRACTIONf_dihedral_angle_d13.9344483
X-RAY DIFFRACTIONf_chiral_restr0.0451718
X-RAY DIFFRACTIONf_plane_restr0.0052067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7803-1.80050.2872240.20624328X-RAY DIFFRACTION97
1.8005-1.82170.23922190.19854497X-RAY DIFFRACTION99
1.8217-1.84390.25782490.19314463X-RAY DIFFRACTION100
1.8439-1.86730.26232100.18944489X-RAY DIFFRACTION100
1.8673-1.89180.23342260.18284511X-RAY DIFFRACTION100
1.8918-1.91780.21612290.17714476X-RAY DIFFRACTION100
1.9178-1.94520.25222390.18134498X-RAY DIFFRACTION100
1.9452-1.97420.21092430.17334468X-RAY DIFFRACTION100
1.9742-2.0050.20552330.17364538X-RAY DIFFRACTION100
2.005-2.03790.19132080.1744511X-RAY DIFFRACTION100
2.0379-2.07310.22422270.17074486X-RAY DIFFRACTION100
2.0731-2.11070.19172210.17224523X-RAY DIFFRACTION100
2.1107-2.15130.20872310.17284517X-RAY DIFFRACTION100
2.1513-2.19530.21842490.17964493X-RAY DIFFRACTION100
2.1953-2.2430.22592250.17474519X-RAY DIFFRACTION100
2.243-2.29520.22772310.1774542X-RAY DIFFRACTION100
2.2952-2.35250.22392270.17774538X-RAY DIFFRACTION100
2.3525-2.41610.19562370.1754508X-RAY DIFFRACTION100
2.4161-2.48720.23282390.18184535X-RAY DIFFRACTION100
2.4872-2.56750.2392310.1874536X-RAY DIFFRACTION100
2.5675-2.65930.23322340.18164524X-RAY DIFFRACTION100
2.6593-2.76570.2162240.18574570X-RAY DIFFRACTION100
2.7657-2.89160.21682310.18714525X-RAY DIFFRACTION100
2.8916-3.0440.21282420.18514586X-RAY DIFFRACTION100
3.044-3.23460.19682230.18454556X-RAY DIFFRACTION100
3.2346-3.48420.20922550.18374591X-RAY DIFFRACTION100
3.4842-3.83460.20582350.16734611X-RAY DIFFRACTION100
3.8346-4.3890.16272420.15134619X-RAY DIFFRACTION100
4.389-5.52760.16112510.14414653X-RAY DIFFRACTION100
5.5276-41.58030.17852480.15634863X-RAY DIFFRACTION100

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