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- PDB-4zs9: Raffinose and panose binding protein from Bifidobacterium animali... -

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Basic information

Entry
Database: PDB / ID: 4zs9
TitleRaffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose
ComponentsSugar binding protein of ABC transporter system
KeywordsTRANSPORT PROTEIN / Raffinose / ABC transporter / complex
Function / homology
Function and homology information


transmembrane transport / metal ion binding
Similarity search - Function
: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
raffinose / Sugar binding protein of ABC transporter system / :
Similarity search - Component
Biological speciesBifidobacterium animalis subsp. lactis Bl-04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsFredslund, F. / Ejby, M. / Andersen, J.M. / Slotboom, D.J. / Abou Hachem, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Denmark
CitationJournal: J. Biol. Chem. / Year: 2016
Title: An ATP Binding Cassette Transporter Mediates the Uptake of alpha-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates.
Authors: Ejby, M. / Fredslund, F. / Andersen, J.M. / Vujicic Zagar, A. / Henriksen, J.R. / Andersen, T.L. / Svensson, B. / Slotboom, D.J. / Abou Hachem, M.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Sugar binding protein of ABC transporter system
B: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,72223
Polymers92,2072
Non-polymers1,51521
Water20,0691114
1
A: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,84911
Polymers46,1041
Non-polymers74510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,87312
Polymers46,1041
Non-polymers77011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.540, 90.820, 146.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sugar binding protein of ABC transporter system


Mass: 46103.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis Bl-04 (bacteria)
Gene: Balac_1599 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE3 / References: UniProt: C6A9Y6, UniProt: A0A1A9TA69*PLUS
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose / raffinose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% PEG 4000, 0.8 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2012
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.37→57 Å / Num. obs: 151108 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1

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Processing

Software
NameVersionClassification
xia2data reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZZA

4zza


Resolution: 1.37→57 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1666 7579 5.02 %Random selection
Rwork0.1324 143271 --
obs0.1341 150850 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.31 Å2 / Biso mean: 19.1672 Å2 / Biso min: 5.61 Å2
Refinement stepCycle: final / Resolution: 1.37→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 0 150 1114 7222
Biso mean--14.59 29.97 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136253
X-RAY DIFFRACTIONf_angle_d1.4228505
X-RAY DIFFRACTIONf_chiral_restr0.21937
X-RAY DIFFRACTIONf_plane_restr0.0091112
X-RAY DIFFRACTIONf_dihedral_angle_d13.3922294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.38560.29722530.24124601485494
1.3856-1.40190.29542420.22654543478594
1.4019-1.4190.2632400.20674629486994
1.419-1.43690.25852390.1994595483494
1.4369-1.45580.23362260.18664466469291
1.4558-1.47580.21582300.16974651488195
1.4758-1.49690.23912700.15834654492495
1.4969-1.51920.19432510.14274638488995
1.5192-1.5430.2062430.13124742498596
1.543-1.56830.19272300.13264697492796
1.5683-1.59530.1792570.12354702495996
1.5953-1.62430.18152590.12054706496596
1.6243-1.65560.17062330.12034776500997
1.6556-1.68940.17922260.11864815504197
1.6894-1.72610.17962300.11814782501297
1.7261-1.76620.16182580.11514720497897
1.7662-1.81040.1682320.11584815504797
1.8104-1.85940.15142880.11764785507397
1.8594-1.91410.16172660.1144791505797
1.9141-1.97590.16792660.11344793505998
1.9759-2.04650.14772430.11324832507598
2.0465-2.12840.14832480.11164853510198
2.1284-2.22530.15522470.11574841508897
2.2253-2.34260.14392760.11584834511098
2.3426-2.48940.14722790.12114899517899
2.4894-2.68160.15722540.13354911516598
2.6816-2.95150.17222580.14034968522699
2.9515-3.37850.1582620.13864976523899
3.3785-4.25630.14842880.12235031531999
4.2563-57.12470.16312850.1555225551099

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