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

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Basic information

Entry
Database: PDB / ID: 4zza
TitleRaffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose, selenomethionine derivative
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 / SAD / Resolution: 2.02 Å
AuthorsFredslund, F. / Ejby, M. / Andersen, J.M. / Slotboom, D.J. / Abou Hachem, M.
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 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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_atom_id / _atom_site.label_comp_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 / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)90,3764
Polymers89,3672
Non-polymers1,0092
Water15,367853
1
A: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1882
Polymers44,6831
Non-polymers5041
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)45,1882
Polymers44,6831
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.385, 90.949, 145.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA5 - 384
211chain BB4 - 383

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Components

#1: Protein Sugar binding protein of ABC transporter system


Mass: 44683.426 Da / Num. of mol.: 2 / Fragment: UNP residues 42-437
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 B (bacteria) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: C6A9Y6, UniProt: A0A1A9TAB8*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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 21% PEG 4000, 1.0 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9805 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 2.02→43 Å / Num. obs: 92158 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.118 / Χ2: 1.496 / Net I/σ(I): 8.67 / Num. measured all: 199614
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.02-2.14.10.8080.4773.533173915087148340.43999
2.14-2.290.890.2373.743019814134140240.31599.2
2.29-2.470.9420.1695.062832813226131110.22599.1
2.47-2.710.9640.1316.442609812088119950.17499.2
2.71-3.020.9820.098.912364610995108840.1299
3.02-3.490.9930.05713.0920918969996000.07799
3.49-4.270.9950.0418.3917711819080770.05498.6
4.27-6.010.9970.03619.8913580633962010.04897.8
6.010.9980.03119.957396352734320.04297.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.02→43 Å / FOM work R set: 0.8846 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2449 5 %Random selection
Rwork0.1685 46532 --
obs0.1706 48981 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.18 Å2 / Biso mean: 15.02 Å2 / Biso min: 3.19 Å2
Refinement stepCycle: final / Resolution: 2.02→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 131 853 6751
Biso mean--9.92 22.02 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125974
X-RAY DIFFRACTIONf_angle_d1.2928111
X-RAY DIFFRACTIONf_chiral_restr0.076893
X-RAY DIFFRACTIONf_plane_restr0.0071057
X-RAY DIFFRACTIONf_dihedral_angle_d13.5622154
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3262X-RAY DIFFRACTION5.004TORSIONAL
12B3262X-RAY DIFFRACTION5.004TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0189-2.06010.23951390.19092655279498
2.0601-2.10490.21631420.179426942836100
2.1049-2.15380.22791420.174226942836100
2.1538-2.20770.20761430.169127202863100
2.2077-2.26740.21381420.165126912833100
2.2674-2.33410.21761420.170627062848100
2.3341-2.40950.20691440.162927322876100
2.4095-2.49560.22251430.166627132856100
2.4956-2.59550.22951440.173227432887100
2.5955-2.71360.22691420.173627012843100
2.7136-2.85660.231450.186427402885100
2.8566-3.03560.23891440.176827412885100
3.0356-3.26990.21361440.168527462890100
3.2699-3.59890.18751450.152627562901100
3.5989-4.11940.17411470.137327882935100
4.1194-5.1890.16631470.14392797294499
5.189-47.3170.23731540.2162915306998

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