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- PDB-5gx8: Crystal structure of solute-binding protein related to glycosamin... -

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Basic information

Entry
Database: PDB / ID: 5gx8
TitleCrystal structure of solute-binding protein related to glycosaminoglycans
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
D(-)-TARTARIC ACID / Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesStreptobacillus moniliformis DSM 12112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.778 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 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,94220
Polymers108,5432
Non-polymers1,39918
Water13,854769
1
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8829
Polymers54,2711
Non-polymers6118
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)55,06011
Polymers54,2711
Non-polymers78910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-44 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.674, 142.050, 73.676
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Extracellular solute-binding protein family 1


Mass: 54271.309 Da / Num. of mol.: 2 / Fragment: UNP residues 28-500
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

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Non-polymers , 5 types, 787 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M tri-sodium citrate dehydrate (pH 5.6), 2M ammonium sulfate

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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: Dec 4, 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: 139193 / % possible obs: 98.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.2
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.407

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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: 1.778→39.364 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 6979 5.02 %
Rwork0.1972 --
obs0.1988 138900 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.778→39.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7653 0 79 769 8501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157945
X-RAY DIFFRACTIONf_angle_d1.24610745
X-RAY DIFFRACTIONf_dihedral_angle_d15.5424735
X-RAY DIFFRACTIONf_chiral_restr0.0781135
X-RAY DIFFRACTIONf_plane_restr0.0081383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7776-1.79780.32122130.26114098X-RAY DIFFRACTION93
1.7978-1.81890.31332150.25164393X-RAY DIFFRACTION100
1.8189-1.84110.27572330.23734457X-RAY DIFFRACTION100
1.8411-1.86440.28132350.234334X-RAY DIFFRACTION100
1.8644-1.8890.28232340.22614413X-RAY DIFFRACTION100
1.889-1.91480.26272030.2194379X-RAY DIFFRACTION100
1.9148-1.94220.28162310.22464434X-RAY DIFFRACTION100
1.9422-1.97120.2852180.22214438X-RAY DIFFRACTION100
1.9712-2.0020.28172280.21544358X-RAY DIFFRACTION100
2.002-2.03480.27372490.21324365X-RAY DIFFRACTION100
2.0348-2.06990.25612520.20584397X-RAY DIFFRACTION100
2.0699-2.10750.25052250.20114458X-RAY DIFFRACTION100
2.1075-2.14810.24512490.19454309X-RAY DIFFRACTION100
2.1481-2.19190.23682050.19664434X-RAY DIFFRACTION100
2.1919-2.23960.24212560.19754392X-RAY DIFFRACTION100
2.2396-2.29170.21992680.18854398X-RAY DIFFRACTION100
2.2917-2.3490.23442170.19394414X-RAY DIFFRACTION100
2.349-2.41250.23462320.19444359X-RAY DIFFRACTION100
2.4125-2.48340.24842370.19954413X-RAY DIFFRACTION100
2.4834-2.56360.22022460.1974403X-RAY DIFFRACTION100
2.5636-2.65520.24362390.20314414X-RAY DIFFRACTION100
2.6552-2.76150.23712420.20484380X-RAY DIFFRACTION100
2.7615-2.88710.24112450.20784405X-RAY DIFFRACTION100
2.8871-3.03930.24762060.21274469X-RAY DIFFRACTION100
3.0393-3.22960.22132130.20554409X-RAY DIFFRACTION100
3.2296-3.47880.21222540.20074426X-RAY DIFFRACTION100
3.4788-3.82870.20282350.1834395X-RAY DIFFRACTION100
3.8287-4.38210.19032390.16714434X-RAY DIFFRACTION100
4.3821-5.51850.1922330.17164450X-RAY DIFFRACTION100
5.5185-39.37390.2092270.19024493X-RAY DIFFRACTION99

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