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

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Basic information

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


transmembrane transport / metal ion binding / plasma membrane
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
Sugar binding protein of ABC transporter system / :
Similarity search - Component
Biological speciesBifidobacterium animalis subsp. lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFredslund, F. / Ejby, M. / Andersen, J.M. / Slotboom, D.J. / Hachem, M.A.
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: 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / 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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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: Sugar binding protein of ABC transporter system
B: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,79817
Polymers88,4292
Non-polymers1,36915
Water17,781987
1
A: Sugar binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9119
Polymers44,2141
Non-polymers6978
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)44,8878
Polymers44,2141
Non-polymers6737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.880, 91.330, 142.050
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: 44214.480 Da / Num. of mol.: 2 / Fragment: UNP residues 46-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis (bacteria)
Strain: Bl-04 / DGCC2908 / RB 4825 / SD5219 / Gene: Balac_1599 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE3 / References: UniProt: C6A9Y6, UniProt: A0A1A9TAB8*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / 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.: 987 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% PEG 4000, 0.8M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97734 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97734 Å / Relative weight: 1
ReflectionResolution: 1.76→23.2 Å / Num. obs: 71009 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.58 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.098 / Χ2: 0.921 / Net I/σ(I): 10.64 / Num. measured all: 241213
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.76-1.813.20.670.6612.0516737521151730.79499.3
1.81-1.860.7650.5452.4716863511550820.65299.4
1.86-1.910.8290.4453.1617416497149440.52799.5
1.91-1.970.8610.3623.7416748481547930.42999.5
1.97-2.030.9110.2874.5816105469846720.3499.4
2.03-2.10.9380.2285.5315145450344520.27198.9
2.1-2.180.9530.1836.4313849438643350.2298.8
2.18-2.270.9670.1577.7214229423142070.18899.4
2.27-2.370.9780.1319.0214222404540310.15599.7
2.37-2.490.9830.1110.5813507388338610.1399.4
2.49-2.620.9870.111.2512723369336670.11899.3
2.62-2.780.990.07913.3211376350934480.09498.3
2.78-2.970.9930.06615.8911205330332880.07899.5
2.97-3.210.9960.05419.5410976308730720.06399.5
3.21-3.520.9970.04123.479929284828400.04999.7
3.52-3.940.9980.03626.488673261525760.04398.5
3.94-4.540.9980.0328.267382230022670.03598.6
4.54-5.570.9990.02828.576782197919570.03398.9
5.57-7.870.9980.03124.944822156215230.03797.5
7.870.9990.02628.1325249348210.03187.9

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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: 1.76→23.113 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 3538 4.99 %Random selection
Rwork0.1578 67402 --
obs0.1602 70940 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.29 Å2 / Biso mean: 21.2313 Å2 / Biso min: 4.52 Å2
Refinement stepCycle: final / Resolution: 1.76→23.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 81 987 7009
Biso mean--14.82 28.94 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056255
X-RAY DIFFRACTIONf_angle_d0.9598506
X-RAY DIFFRACTIONf_chiral_restr0.041941
X-RAY DIFFRACTIONf_plane_restr0.0051110
X-RAY DIFFRACTIONf_dihedral_angle_d13.9062338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.78410.26341310.25112656278799
1.7841-1.80960.28151330.241326692802100
1.8096-1.83660.27811510.2332667281899
1.8366-1.86530.28961420.220726642806100
1.8653-1.89580.26781360.213526922828100
1.8958-1.92850.25121500.20182647279799
1.9285-1.96360.25911490.19392664281399
1.9636-2.00130.24841330.180426792812100
2.0013-2.04210.22971240.17672702282699
2.0421-2.08650.22761520.17082671282399
2.0865-2.1350.22421350.16232638277399
2.135-2.18840.23211460.16272689283599
2.1884-2.24750.20581250.158926822807100
2.2475-2.31360.22381510.14822704285599
2.3136-2.38820.18141390.145926932832100
2.3882-2.47340.17971410.141726912832100
2.4734-2.57230.23591420.1482685282799
2.5723-2.68920.19471460.1482701284799
2.6892-2.83080.22951450.1532655280098
2.8308-3.00780.16991390.154427492888100
3.0078-3.23940.22821470.14682731287899
3.2394-3.56440.17561380.136927472885100
3.5644-4.07770.1491440.12062709285398
4.0777-5.12820.14251510.12422788293999
5.1282-23.1150.21471480.17862829297797

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