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- PDB-6pre: SBP RafE in complex with verbascose -

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Basic information

Entry
Database: PDB / ID: 6pre
TitleSBP RafE in complex with verbascose
ComponentsABC transporter sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Cluster D-I solute binding protein / complex / SBP
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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 / Sugar ABC transporter, sugar-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMeier, E.P.W. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular analysis of an enigmaticStreptococcus pneumoniaevirulence factor: The raffinose-family oligosaccharide utilization system.
Authors: Hobbs, J.K. / Meier, E.P.W. / Pluvinage, B. / Mey, M.A. / Boraston, A.B.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / 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_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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: ABC transporter sugar-binding protein
B: ABC transporter sugar-binding protein
C: ABC transporter sugar-binding protein
D: ABC transporter sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1379
Polymers185,7604
Non-polymers3,3775
Water5,477304
1
A: ABC transporter sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2692
Polymers46,4401
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3313
Polymers46,4401
Non-polymers8912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC transporter sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2692
Polymers46,4401
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC transporter sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2692
Polymers46,4401
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.918, 145.877, 118.371
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ABC transporter sugar-binding protein / Sugar ABC transporter binding protein


Mass: 46440.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1897 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E8ZWG6, UniProt: A0A0H2URJ7*PLUS
#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-[beta-D- ...alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-[beta-D-fructofuranose-(2-1)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DGalpa1-6DGalpa1-6[DFrufb2-1]DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3-3/a2-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{[(6+1)][a-D-Galp]{[(6+1)][a-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M MnCl2, 0.2M CsCl, 0.1M Tris, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 64353 / % possible obs: 99.6 % / Redundancy: 4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.076 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 4289 / CC1/2: 0.706 / Rpim(I) all: 0.344

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PRG

6prg


Resolution: 2.4→29.55 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.919 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.598 / ESU R Free: 0.3 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 3024 4.7 %RANDOM
Rwork0.2314 ---
obs0.2332 60863 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 36.913 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.18 Å2
2---0.49 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2.4→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11892 0 228 304 12424
Biso mean--36.52 31.39 -
Num. residues----1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01212415
X-RAY DIFFRACTIONr_angle_refined_deg0.6451.66716939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.38551536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68624.809601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.036151902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6721532
X-RAY DIFFRACTIONr_chiral_restr0.0510.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029468
LS refinement shellResolution: 2.4→2.459 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 213 -
Rwork0.314 3860 -
obs--84.57 %

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