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- PDB-5suo: Crystal structure of N-glycan transport solute binding protein (N... -

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Basic information

Entry
Database: PDB / ID: 5suo
TitleCrystal structure of N-glycan transport solute binding protein (NgtS) from Streptococcus pneumoniae
ComponentsExtracellular solute-binding protein
KeywordsPROTEIN BINDING / Solute binding protein / alpha/beta domain
Function / homologyIODIDE ION / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsRobb, M. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 130305 Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence.
Authors: Robb, M. / Hobbs, J.K. / Woodiga, S.A. / Shapiro-Ward, S. / Suits, M.D. / McGregor, N. / Brumer, H. / Yesilkaya, H. / King, S.J. / Boraston, A.B.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,33722
Polymers50,6721
Non-polymers2,66521
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.910, 40.200, 93.890
Angle α, β, γ (deg.)90.000, 98.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Extracellular solute-binding protein


Mass: 50671.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ERS020541_01426, ERS558328_01721 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0T7JX40
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29 % PEG 1500, 11 % 2-methyl-2,4-pentanediol, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.73→92.79 Å / Num. obs: 25262 / % possible obs: 99.9 % / Redundancy: 4.7 % / Net I/σ(I): 25.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→92.79 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.504 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.215 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1339 5 %RANDOM
Rwork0.211 ---
obs0.2136 25262 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.09 Å2 / Biso mean: 19.711 Å2 / Biso min: 4.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.1→92.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 21 227 3734
Biso mean--39.3 19.25 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023561
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9614834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72626.312160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30215605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.699156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212697
X-RAY DIFFRACTIONr_mcbond_it1.1011.9631804
X-RAY DIFFRACTIONr_mcangle_it1.8652.9362252
X-RAY DIFFRACTIONr_scbond_it1.2682.0211757
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 114 -
Rwork0.242 1783 -
all-1897 -
obs--99.27 %

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