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- PDB-9h0p: Fucosylated Lacto-N-biose binding protein from Bifidobacterium lo... -

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Basic information

Entry
Database: PDB / ID: 9h0p
TitleFucosylated Lacto-N-biose binding protein from Bifidobacterium longum subsp. infantis in complex with H1 trisaccharide
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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)49,1282
Polymers48,5991
Non-polymers5291
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint14 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.906, 95.906, 114.768
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#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 alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.7→67.29 Å / Num. obs: 27544 / % possible obs: 99.87 % / Redundancy: 20 % / Biso Wilson estimate: 32.44 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.528 / Rpim(I) all: 0.118 / Rrim(I) all: 0.541 / Net I/σ(I): 5.85
Reflection shellResolution: 2.7→2.87 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 4517 / CC1/2: 0.52 / Rpim(I) all: 0.658 / Rrim(I) all: 1 / Rsym value: 1 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→67.29 Å / SU ML: 0.2638 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 861 5 %
Rwork0.1711 16356 -
obs0.174 17217 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.54 Å2
Refinement stepCycle: LAST / Resolution: 2.7→67.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 36 143 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323259
X-RAY DIFFRACTIONf_angle_d0.59534425
X-RAY DIFFRACTIONf_chiral_restr0.0423497
X-RAY DIFFRACTIONf_plane_restr0.0031562
X-RAY DIFFRACTIONf_dihedral_angle_d21.00731243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.29151410.20872690X-RAY DIFFRACTION99.89
2.87-3.090.32681410.22562680X-RAY DIFFRACTION99.89
3.09-3.40.24981420.18372693X-RAY DIFFRACTION99.79
3.4-3.890.20061420.17142689X-RAY DIFFRACTION99.96
3.89-4.910.21051440.13552749X-RAY DIFFRACTION100
4.91-67.290.19311510.16082855X-RAY DIFFRACTION99.7
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)
10.0420622967371-0.0161894620769-0.07044224084110.03209257246690.03013478862250.1155233660990.0492369634272-0.1236611680610.0307654491803-0.0707551489964-0.02163747311330.04621821502570.05567480376460.04041150982649.23943849346E-60.229893696713-0.0461272479949-0.02864814242860.215115251764-0.04657762483740.185331482314-28.230135123443.817594880415.2525872907
20.2597563873510.10243651382-0.1712346760080.213047978855-0.078206938430.1130318031050.148834174555-0.2525942897780.1183225849750.399594302121-0.1421059031780.148024016371-0.450727402893-0.001003460689280.0006078101080210.3879407148040.07990101554010.03863984314420.351849195043-0.01523548804520.221408047584-40.456145404551.817061367214.858149809
30.05698800514260.0565877303480.09296511828360.302304432477-0.1380827784790.371141763259-0.04231328485280.220306288210.09881751171250.04423270777810.01530249011080.0978503877228-0.132648248035-0.00956037834240.0115851642470.137836146115-0.0482760432269-0.01577005014580.243619796013-0.027594332850.173026717098-35.677751941543.31321893980.639914487041
40.1264641350550.09627453405520.07128917077010.077320080210.06980673359710.0892328733609-0.01539062308310.1035474114320.08115147774970.02429839917860.02021808448440.1348582497810.0384067068405-0.009912984938215.277909686E-60.213998674289-0.0154545298992-0.002005558813520.1646214463270.01598925650570.249661793818-48.698435645222.57925606717.24087143816
50.3213599106880.09964921048170.1221275705340.3096406096620.07699019484340.092142252867-0.0413875406404-0.0329789155510.0407111888246-0.016260054998-0.0860114591540.05584998866740.144702081319-0.218543417045-0.0001937668146510.181133998962-0.0007799479956870.004269837691240.155324276884-0.006384380762150.217644664375-56.473084153626.30016927788.75927003533
60.431402634657-0.2169791206950.1177517201570.128627309641-0.1032438591060.1851567704790.06365901773540.0301816347021-0.0997868795435-0.0465864746021-0.12334004824-0.126756640767-0.00970542763137-0.0205174482806-0.0005204430574020.268052076813-0.01275589458980.02594211090820.169753054453-0.007810238270270.261347014511-42.059837309126.263281491810.1338327237
70.0119986387410.03705806776230.005449166464720.1095988933890.01783848458990.04905395359420.09179922238190.123576044339-0.1541836843510.292073600084-0.104310391743-0.0528545555505-0.05215318196040.2707665384260.004577777251830.154416062212-0.02242789740480.002823663200080.195638326599-0.002181465124290.191532862344-26.337540467940.42868039176.63766649947
80.0781109787489-0.0465717048219-0.1125017778740.172152332490.04155288734510.1640090621560.0735520044804-0.0266639450882-0.01132478831630.00684758619973-0.0419294271585-0.1933506923310.269377851960.128650175549-0.01113821616590.2856793457840.007380950538290.03842958030340.274447653474-0.04552259308580.21051316246-34.028065833121.7451700023.24257942191
90.0462642380225-0.1265043917840.1058850429220.336136675589-0.2827210760250.237024171219-0.0360014725642-0.1724760286850.2026497745710.2935514860170.0534035348678-0.0642817463665-0.35019737493-0.258883145665-0.009994204674120.2326386658490.0389136522096-0.01950271084060.353554756698-0.02257491268810.217937055586-61.478999154637.24658576134.93460163027
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 38 through 77 )38 - 771 - 40
22chain 'A' and (resid 78 through 96 )78 - 9641 - 59
33chain 'A' and (resid 97 through 141 )97 - 14160 - 104
44chain 'A' and (resid 142 through 222 )142 - 222105 - 185
55chain 'A' and (resid 223 through 284 )223 - 284186 - 247
66chain 'A' and (resid 285 through 338 )285 - 338248 - 301
77chain 'A' and (resid 339 through 361 )339 - 361302 - 324
88chain 'A' and (resid 362 through 393 )362 - 393325 - 356
99chain 'A' and (resid 394 through 442 )394 - 442357 - 406

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