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- PDB-5gx6: Crystal structure of solute-binding protein complexed with unsatu... -

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Basic information

Entry
Database: PDB / ID: 5gx6
TitleCrystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-4 position of GalNAc
ComponentsExtracellular solute-binding protein family 1
KeywordsSUGAR BINDING PROTEIN / glycosaminoglycan / ABC transporter / solute-binding protein
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
: / 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
Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesStreptobacillus moniliformis DSM 12112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsOiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aid 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
DepositionSep 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.ptnr2_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)168,16524
Polymers165,7363
Non-polymers2,42921
Water17,366964
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0558
Polymers55,2451
Non-polymers8107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,17910
Polymers55,2451
Non-polymers9349
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9316
Polymers55,2451
Non-polymers6865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.983, 112.590, 165.928
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 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 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-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 459.380 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][a-L-4-deoxy-IdopA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M HEPES (pH 7.0), 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 136919 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 37.5
Reflection shellResolution: 1.81→1.84 Å / Rmerge(I) obs: 0.519

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data processing
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GUB

5gub


Resolution: 1.81→39.453 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 6848 5.03 %
Rwork0.191 --
obs0.1921 136214 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→39.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11499 0 153 964 12616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912087
X-RAY DIFFRACTIONf_angle_d1.12516348
X-RAY DIFFRACTIONf_dihedral_angle_d15.5647234
X-RAY DIFFRACTIONf_chiral_restr0.0641742
X-RAY DIFFRACTIONf_plane_restr0.0062098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8098-1.83040.27962080.23114159X-RAY DIFFRACTION97
1.8304-1.85190.27552210.22844284X-RAY DIFFRACTION100
1.8519-1.87450.23272220.21154264X-RAY DIFFRACTION100
1.8745-1.89820.24952200.20554283X-RAY DIFFRACTION100
1.8982-1.92320.24162270.20044236X-RAY DIFFRACTION99
1.9232-1.94960.24452300.19994278X-RAY DIFFRACTION99
1.9496-1.97740.24812150.1984291X-RAY DIFFRACTION99
1.9774-2.00690.21872180.19824285X-RAY DIFFRACTION100
2.0069-2.03830.23662080.19854256X-RAY DIFFRACTION99
2.0383-2.07170.23612430.19614256X-RAY DIFFRACTION99
2.0717-2.10740.22112280.19674272X-RAY DIFFRACTION99
2.1074-2.14580.24842400.20274231X-RAY DIFFRACTION99
2.1458-2.1870.23672270.20334278X-RAY DIFFRACTION99
2.187-2.23170.23172430.19194279X-RAY DIFFRACTION99
2.2317-2.28020.21982370.19174274X-RAY DIFFRACTION100
2.2802-2.33320.22512230.18994296X-RAY DIFFRACTION100
2.3332-2.39160.23392450.20244271X-RAY DIFFRACTION99
2.3916-2.45620.2052430.1954278X-RAY DIFFRACTION100
2.4562-2.52850.2612270.24308X-RAY DIFFRACTION100
2.5285-2.61010.21422340.19784316X-RAY DIFFRACTION100
2.6101-2.70330.22191780.20224370X-RAY DIFFRACTION100
2.7033-2.81150.22912310.19954333X-RAY DIFFRACTION100
2.8115-2.93950.21282470.20134322X-RAY DIFFRACTION100
2.9395-3.09440.22062320.24352X-RAY DIFFRACTION100
3.0944-3.28820.17572110.20214388X-RAY DIFFRACTION100
3.2882-3.54190.21042290.19674371X-RAY DIFFRACTION100
3.5419-3.8980.17552140.1794381X-RAY DIFFRACTION100
3.898-4.46140.17832380.16464427X-RAY DIFFRACTION100
4.4614-5.61840.16832620.15994414X-RAY DIFFRACTION100
5.6184-39.46280.17942470.17224613X-RAY DIFFRACTION99

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