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- PDB-9h0o: Fucosylated Lacto-N-biose binding protein from Bifidobacterium lo... -

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Basic information

Entry
Database: PDB / ID: 9h0o
TitleFucosylated Lacto-N-biose binding protein from Bifidobacterium longum subsp. infantis in complex with Lacto-N-biose
ComponentsExtracellular solute-binding protein, family 1
KeywordsTRANSPORT PROTEIN / Solute binding protein / ABC importer / HMO capture / Bifidobacterium longum subsp. infantis
Function / homologyCarbohydrate ABC transporter substrate-binding, CPR0540 / : / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / plasma membrane / : / Extracellular solute-binding protein, family 1
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsJensen, M. / Hansen, M.E. / Sakanaka, H. / Slotboom, D.J. / Abou Hachem, M. / Morth, J.P.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Other private4002-00297B Denmark
Other private1026-00386B Denmark
Citation
Journal: Mbio / Year: 2025
Title: Uptake of fucosylated type I human milk oligosaccharide blocks by Bifidobacterium longum subsp. infantis
Authors: Hansen, M.E. / Sakanaka, M. / Jensen, M. / Sakanaka, H. / Pichler, M.J. / Maeda, S. / Hoevring, J.F. / Nakajima, A. / Kunstmann, S. / Nielsen, T.S. / Peters, G.H.J. / Slotboom, D.J. / Morth, ...Authors: Hansen, M.E. / Sakanaka, M. / Jensen, M. / Sakanaka, H. / Pichler, M.J. / Maeda, S. / Hoevring, J.F. / Nakajima, A. / Kunstmann, S. / Nielsen, T.S. / Peters, G.H.J. / Slotboom, D.J. / Morth, J.P. / Katayama, T. / Abou Hachem, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1646
Polymers48,5991
Non-polymers5655
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-43 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.070, 52.560, 149.319
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

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 48598.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Gene: Blon_0883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7GQA3
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: An amino disaccharide consisting of beta-D-galactose (GAL) linked via a (1-3)-glycosidic bond to N-acetyl-D-glucosamine (NDG).
References: BIRD: PRD_002584
DescriptorTypeProgram
DGalpb1-3DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 367 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsLacto-N-biose I (LNB; Gal-beta-1-3GlcNAc; GalB1-3GlcNAc) disaccharide is present as a core unit of ...Lacto-N-biose I (LNB; Gal-beta-1-3GlcNAc; GalB1-3GlcNAc) disaccharide is present as a core unit of type-1 blood group antigens of animal glycoconjugates and milk oligosaccharides.
Has ligand of interestY
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaCl, 0.1 M Tris pH 7.0, 30% PEG3000 + TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 2.075 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.075 Å / Relative weight: 1
ReflectionResolution: 2.14→49.58 Å / Num. obs: 21409 / % possible obs: 95.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 38.23 Å2 / Net I/σ(I): 10.35
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 1112

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→49.58 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 2000 5.03 %
Rwork0.2015 37740 -
obs0.2033 21409 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.23 Å2
Refinement stepCycle: LAST / Resolution: 2.14→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 34 363 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143261
X-RAY DIFFRACTIONf_angle_d0.37834425
X-RAY DIFFRACTIONf_chiral_restr0.0357493
X-RAY DIFFRACTIONf_plane_restr0.0026563
X-RAY DIFFRACTIONf_dihedral_angle_d10.17161224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.20.40841020.38871906X-RAY DIFFRACTION66.82
2.2-2.260.33971250.34692423X-RAY DIFFRACTION85.39
2.26-2.320.31871340.32222617X-RAY DIFFRACTION93.51
2.32-2.40.33281500.29182794X-RAY DIFFRACTION97.45
2.4-2.480.30221500.26192779X-RAY DIFFRACTION98.69
2.48-2.580.27361480.24482806X-RAY DIFFRACTION99.13
2.58-2.70.30431490.23582781X-RAY DIFFRACTION98.89
2.7-2.840.27191430.21972800X-RAY DIFFRACTION98.99
2.84-3.020.24031480.22062821X-RAY DIFFRACTION98.8
3.02-3.260.24741460.20812796X-RAY DIFFRACTION99.19
3.26-3.580.23961500.17952816X-RAY DIFFRACTION99.23
3.58-4.10.21381470.16392770X-RAY DIFFRACTION98.41
4.1-5.170.16961560.15332830X-RAY DIFFRACTION99.53
5.17-49.580.19181520.1662801X-RAY DIFFRACTION99.13
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5054231203860.0828691570620.3258195118370.0931472100152-0.002874966603220.249473333023-0.0373494045247-0.2598569551450.1560727764810.2290958410340.0115602238496-0.064817687643-0.3179670757620.347562539482-0.000106171698880.4394874308150.02995933583970.000125139119760.439645074379-0.00468979524410.38282120670231.513598832236.887031851750.1738947916
20.1079163050740.007715170169070.02075193785330.007905616056630.0002177928634650.0533877043028-0.100672649459-0.1361985710450.2412177602620.1125300901370.229414271489-0.0187417033546-0.0169058549930.129412041099-9.62192601274E-50.635343609886-0.06743423740250.05035147523120.554657188241-0.09130586075030.56937210016924.944377075546.809988081158.7416736617
30.4536410947070.105945828003-0.1012834539490.6612206905210.466865438290.5545780980020.04388217476750.02354480147940.04037240820540.0608157211991-0.02887589330870.0909449973944-0.0585573101539-0.0217694719857-1.84961818706E-50.3628513138950.0588363264172-0.01022908776370.3710425456240.02026847286370.35424924018910.171192075927.530967838855.3347753423
40.1385762555980.02433893745250.02549789856670.07948838477710.08339441203580.08733673591220.1840473402410.1128247277160.06243668336450.1527164849340.008131726391580.549506835020.0440939618059-0.08739206022770.0005004905164810.3925805289040.05564356758140.07361052870010.450089632850.08868560195420.585904602404-5.8370526971629.738767744161.6791993849
50.4119435176180.00853356944644-0.02110724377590.180499819632-0.2134128364990.2552433094840.03968680087510.015821029492-0.04420347118240.1261838452460.0189306391779-0.0548247024337-0.100611123858-0.03194600243013.62927205227E-50.4909390392310.02545361204510.02072529568130.3710588961760.004223397556750.35287461901917.089080621725.01663872758.5151703957
60.553859722030.06170509717450.1933248514590.611506564109-0.429156297510.401849134101-0.0746951296126-0.0554528599212-0.03726441114790.07910922276580.1750626095540.17716541363-0.0240353010878-0.02370537202943.75831237621E-50.4356922620310.02834823608010.05755163048720.3785230173150.02970530441410.4403873649665.0082998062230.03384326158.6636863427
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 77 )37 - 771 - 41
22chain 'A' and (resid 78 through 96 )78 - 9642 - 60
33chain 'A' and (resid 97 through 221 )97 - 22161 - 185
44chain 'A' and (resid 222 through 256 )222 - 256186 - 220
55chain 'A' and (resid 257 through 361 )257 - 361221 - 325
66chain 'A' and (resid 362 through 442 )362 - 442326 - 407

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