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- PDB-6q5g: The ABC transporter associated binding protein from B. animalis s... -

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Basic information

Entry
Database: PDB / ID: 6q5g
TitleThe ABC transporter associated binding protein from B. animalis subsp. lactis Bl-04 without ligand. SeMet variant
ComponentsSugar ABC transporter substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / complex / ABC transporter / phasing
Function / homologyBacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / transmembrane transport / ABC transporter substrate-binding protein / :
Function and homology information
Biological speciesBifidobacterium animalis subsp. lactis BB-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFredslund, F. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4002-00297 Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate preference of an ABC importer corresponds to selective growth on beta-(1,6)-galactosides inBifidobacterium animalissubsp.lactis.
Authors: Theilmann, M.C. / Fredslund, F. / Svensson, B. / Lo Leggio, L. / Abou Hachem, M.
History
DepositionDec 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein
B: Sugar ABC transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)93,4452
Polymers93,4452
Non-polymers00
Water10,845602
1
A: Sugar ABC transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)46,7231
Polymers46,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)46,7231
Polymers46,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.935, 69.364, 97.297
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sugar ABC transporter substrate-binding protein


Mass: 46722.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selenomethionine variant
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis BB-12 (bacteria)
Gene: DU497_02550 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A386JXS7, UniProt: A0A1C7FWS9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MDP, 30 mM each of di-,tri-,tetra- and pentaethyleneglycol with 0.1M MES/imidazole at pH6.5
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 54411 / % possible obs: 98.87 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09542 / Net I/σ(I): 13.35
Reflection shellResolution: 2→2.071 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSol1.11.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.113 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2004 1012 1.86 %
Rwork0.1774 --
obs0.1778 54407 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 0 602 7041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036630
X-RAY DIFFRACTIONf_angle_d0.5518996
X-RAY DIFFRACTIONf_dihedral_angle_d13.7883868
X-RAY DIFFRACTIONf_chiral_restr0.04936
X-RAY DIFFRACTIONf_plane_restr0.0031177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10550.2831360.23417164X-RAY DIFFRACTION93
2.1055-2.23740.25051450.20267674X-RAY DIFFRACTION100
2.2374-2.41010.22651450.19067628X-RAY DIFFRACTION100
2.4101-2.65260.24091450.19847675X-RAY DIFFRACTION100
2.6526-3.03640.25851460.19697692X-RAY DIFFRACTION100
3.0364-3.82530.19391460.17147708X-RAY DIFFRACTION100
3.8253-47.12640.14441490.14897854X-RAY DIFFRACTION100

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