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- PDB-5gx7: Crystal structure of solute-binding protein complexed with unsatu... -

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Basic information

Entry
Database: PDB / ID: 5gx7
TitleCrystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc
ComponentsExtracellular solute-binding protein family 1
KeywordsTRANSPORT PROTEIN / glycosaminoglycan / ABC transporter / solute-binding protein
Function / homologyBacterial 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 / metal ion binding / Alpha Beta / Extracellular solute-binding protein family 1
Function and homology information
Biological speciesStreptobacillus moniliformis DSM 12112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 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 19, 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)167,2349
Polymers165,7363
Non-polymers1,4986
Water13,637757
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7453
Polymers55,2451
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint9 kcal/mol
Surface area20230 Å2
MethodPISA
2
B: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7453
Polymers55,2451
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint10 kcal/mol
Surface area20310 Å2
MethodPISA
3
C: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7453
Polymers55,2451
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint8 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.275, 112.444, 166.614
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-6-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_6*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc6SO3]{[(3+1)][a-L-4-deoxy-ArapA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium thiocyanate, 20% PEG 3350

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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: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 103364 / % possible obs: 98.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 36.3
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.406

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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: 1.991→45.673 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 5067 5.02 %
Rwork0.1967 --
obs0.1994 100999 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.991→45.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11499 0 93 757 12349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211862
X-RAY DIFFRACTIONf_angle_d1.54516062
X-RAY DIFFRACTIONf_dihedral_angle_d16.4417092
X-RAY DIFFRACTIONf_chiral_restr0.091719
X-RAY DIFFRACTIONf_plane_restr0.012061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9905-2.01310.25921570.20532530X-RAY DIFFRACTION78
2.0131-2.03680.29551530.20633101X-RAY DIFFRACTION95
2.0368-2.06170.29911650.21663158X-RAY DIFFRACTION96
2.0617-2.08780.26711460.21543091X-RAY DIFFRACTION96
2.0878-2.11520.29781570.20783158X-RAY DIFFRACTION96
2.1152-2.14420.3011600.21463127X-RAY DIFFRACTION97
2.1442-2.17480.31961590.21583180X-RAY DIFFRACTION97
2.1748-2.20730.34261650.28663050X-RAY DIFFRACTION94
2.2073-2.24180.41931610.31263030X-RAY DIFFRACTION93
2.2418-2.27850.35921820.31653089X-RAY DIFFRACTION95
2.2785-2.31780.40731570.27663052X-RAY DIFFRACTION94
2.3178-2.360.28431690.20943217X-RAY DIFFRACTION98
2.36-2.40540.27861690.20933208X-RAY DIFFRACTION98
2.4054-2.45450.26411590.2023212X-RAY DIFFRACTION98
2.4545-2.50780.27341680.20653255X-RAY DIFFRACTION99
2.5078-2.56620.27681690.20673201X-RAY DIFFRACTION99
2.5662-2.63030.27681590.20093242X-RAY DIFFRACTION99
2.6303-2.70140.26921470.20523275X-RAY DIFFRACTION99
2.7014-2.78090.23991690.21363249X-RAY DIFFRACTION99
2.7809-2.87070.25421790.21763270X-RAY DIFFRACTION99
2.8707-2.97320.28241600.21643284X-RAY DIFFRACTION100
2.9732-3.09230.25321650.21943304X-RAY DIFFRACTION100
3.0923-3.2330.25711920.22473277X-RAY DIFFRACTION100
3.233-3.40340.26631790.21763285X-RAY DIFFRACTION100
3.4034-3.61650.25741920.20643268X-RAY DIFFRACTION99
3.6165-3.89560.22421980.17923265X-RAY DIFFRACTION99
3.8956-4.28740.18961880.1533323X-RAY DIFFRACTION100
4.2874-4.90710.17871800.12533349X-RAY DIFFRACTION100
4.9071-6.18010.16571860.14153388X-RAY DIFFRACTION100
6.1801-45.68480.17061770.14083494X-RAY DIFFRACTION99

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