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- PDB-6fth: HMO binding ABC-transporter associated Solute Binding Protein, Bl... -

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Basic information

Entry
Database: PDB / ID: 6fth
TitleHMO binding ABC-transporter associated Solute Binding Protein, Blon_2347 From Bifidobacterium longum infantis ATCC 15697
ComponentsExtracellular solute-binding protein, family 1
KeywordsSUGAR BINDING PROTEIN / extracellular solute-binding protein / family 1 / Bifidobacterium longum subsp. infantis ATCC 15697
Function / homology: / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta / Extracellular solute-binding protein, family 1
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46851433536 Å
AuthorsEjby, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-00297 Denmark
CitationJournal: Not published
Title: HMO binding ABC-transporter associated Solute Binding Protein, Blon_2347 From Bifidobacterium longum infantis ATCC 15697
Authors: Ejby, M.
History
DepositionFeb 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein, family 1


Theoretical massNumber of molelcules
Total (without water)57,5121
Polymers57,5121
Non-polymers00
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.399, 70.139, 121.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Extracellular solute-binding protein, family 1


Mass: 57511.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Gene: Blon_2347 / Plasmid: pETM-11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B7GNP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.12 Å3/Da / Density % sol: 42.09 % / Description: Rod shaped
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.468→45.9 Å / Num. obs: 149050 / % possible obs: 96.12 % / Redundancy: 12.6 % / Biso Wilson estimate: 15.8181883171 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1084 / Rrim(I) all: 0.113 / Net I/σ(I): 16.44
Reflection shellResolution: 1.469→1.522 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.963 / Num. unique obs: 5197 / CC1/2: 0.897 / Rrim(I) all: 1.013 / % possible all: 64.74

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OMB

3omb


Resolution: 1.46851433536→45.8381348526 Å / SU ML: 0.145601682509 / Cross valid method: FREE R-VALUE / σ(F): 1.33286008293 / Phase error: 18.2464963816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186774863502 7464 5.01464620677 %
Rwork0.159647648506 141380 -
obs0.160998932361 148844 95.6335132357 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5137986171 Å2
Refinement stepCycle: LAST / Resolution: 1.46851433536→45.8381348526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 0 536 4438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008277314762494002
X-RAY DIFFRACTIONf_angle_d0.974276924915435
X-RAY DIFFRACTIONf_chiral_restr0.0780338910608578
X-RAY DIFFRACTIONf_plane_restr0.00664025030003709
X-RAY DIFFRACTIONf_dihedral_angle_d13.13096573991455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4685-1.48520.960211457795210.890952232121447X-RAY DIFFRACTION9.19630575752
1.4852-1.50270.3790253039131940.3366909735283674X-RAY DIFFRACTION74.6141975309
1.5027-1.5210.288703943642650.2533337525294902X-RAY DIFFRACTION98.606870229
1.521-1.54030.236414616162560.2470559858984823X-RAY DIFFRACTION97.2615855994
1.5403-1.56050.2592638676952550.2415608884634786X-RAY DIFFRACTION98.9013144987
1.5605-1.58190.2662866338642590.2328848061364823X-RAY DIFFRACTION97.6556495004
1.5819-1.60450.2456245746252570.2209071213974890X-RAY DIFFRACTION99.4013132484
1.6045-1.62850.215775163962560.2230519161684904X-RAY DIFFRACTION98.4357115605
1.6285-1.65390.259518392432590.2186942416954876X-RAY DIFFRACTION99.6506889191
1.6539-1.6810.2326973085462590.2042802717884912X-RAY DIFFRACTION98.7963316775
1.681-1.710.2292590394572590.1962156805794917X-RAY DIFFRACTION99.7879313669
1.71-1.74110.2219642089842540.1862845916964823X-RAY DIFFRACTION98.8897545773
1.7411-1.77460.1979355855812610.1839159179194928X-RAY DIFFRACTION99.8652809854
1.7746-1.81080.2316786080182540.18709753774857X-RAY DIFFRACTION99.4357976654
1.8108-1.85020.2165969378632650.1774434107754961X-RAY DIFFRACTION99.5807926829
1.8502-1.89320.1748541432882610.1728644458044929X-RAY DIFFRACTION99.9422299249
1.8932-1.94060.2140525533532590.1649228334734914X-RAY DIFFRACTION99.7108712413
1.9406-1.9930.190648569462590.1569380939494910X-RAY DIFFRACTION99.7683844818
1.993-2.05170.177289610372620.1460190537284947X-RAY DIFFRACTION99.8849472675
2.0517-2.11790.1716787197082580.140420982894911X-RAY DIFFRACTION99.9419953596
2.1179-2.19360.167636618792590.1376464578894899X-RAY DIFFRACTION99.9031570792
2.1936-2.28140.1592944998582610.1343387795614936X-RAY DIFFRACTION99.9615310637
2.2814-2.38530.1642707909422580.1329548898154913X-RAY DIFFRACTION99.9806651199
2.3853-2.5110.1414957609162640.1355115818644949X-RAY DIFFRACTION99.9233275829
2.511-2.66830.1597644976182560.1338865928644894X-RAY DIFFRACTION99.9223903764
2.6683-2.87430.1355655751182630.1349812099834931X-RAY DIFFRACTION99.961508853
2.8743-3.16350.1796613310262590.1406854392764924X-RAY DIFFRACTION100
3.1635-3.62110.16451822422590.1364910053494927X-RAY DIFFRACTION99.9807210334
3.6211-4.56160.1679813079182480.1393543408564931X-RAY DIFFRACTION99.9613974136
4.5616-45.86050.2278721308532640.1881298047724942X-RAY DIFFRACTION100

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