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- PDB-22hh: Beta-1,2-glucan-binding protein complex with linear beta-1,2-glucan -

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Basic information

Entry
Database: PDB / ID: 22hh
TitleBeta-1,2-glucan-binding protein complex with linear beta-1,2-glucan
ComponentsExtracellular solute-binding protein family 1
KeywordsSUGAR BINDING PROTEIN / carbohydrate-binding protein
Function / homology
Function and homology information


glycerophosphodiester transmembrane transport / glycerol-3-phosphate transmembrane transport / cell envelope / transmembrane transporter activity / membrane
Similarity search - Function
: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
beta-D-glucopyranose / Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesChloroflexus aurantiacus Y-400-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNakajima, M. / Kaneko, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2026
Title: Structural and thermodynamic analyses of a novel beta-1,2-glucan binding mode in the ABC transporter solute-binding protein Chy400_4166 from Chloroflexus aurantiacus.
Authors: Kato, K. / Kaneko, T. / Hirayama, R. / Tanaka, N. / Nakai, H. / Torigoe, H. / Nakajima, M.
History
DepositionJan 11, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: 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)55,61811
Polymers53,0531
Non-polymers2,56410
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.710, 83.261, 94.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular solute-binding protein family 1 / Beta-1 / 2-glucan-binding protein


Mass: 53053.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus Y-400-fl (bacteria)
Gene: Caur_3857 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WCS2

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1639.423 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,10,9/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 351 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, bis-Tris, linear beta-1,2-glucan

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→47.63 Å / Num. obs: 88131 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 18.2
Reflection shellResolution: 1.53→1.56 Å / Num. unique obs: 4318 / CC1/2: 0.742 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→47.628 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1756 4385 4.98 %
Rwork0.1584 83668 -
all0.159 --
obs-88053 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.009 Å20 Å20 Å2
2--0.004 Å2-0 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 1.53→47.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 169 343 3896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123727
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163374
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.8045078
X-RAY DIFFRACTIONr_angle_other_deg0.9821.7397788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.566518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56710567
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.810184
X-RAY DIFFRACTIONr_chiral_restr0.0930.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024378
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02874
X-RAY DIFFRACTIONr_nbd_refined0.3270.2778
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.23076
X-RAY DIFFRACTIONr_nbtor_refined0.190.21858
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21795
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.217
X-RAY DIFFRACTIONr_nbd_other0.2250.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.215
X-RAY DIFFRACTIONr_mcbond_it1.7371.7371740
X-RAY DIFFRACTIONr_mcbond_other1.7311.7371740
X-RAY DIFFRACTIONr_mcangle_it2.4573.1192189
X-RAY DIFFRACTIONr_mcangle_other2.4583.1212190
X-RAY DIFFRACTIONr_scbond_it3.2012.1171987
X-RAY DIFFRACTIONr_scbond_other3.22.1181988
X-RAY DIFFRACTIONr_scangle_it4.8363.7322889
X-RAY DIFFRACTIONr_scangle_other4.8353.7332890
X-RAY DIFFRACTIONr_lrange_it5.419.8314336
X-RAY DIFFRACTIONr_lrange_other5.419.8344337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.53-1.570.2723150.24561670.24664840.950.95999.96920.214
1.57-1.6130.2423330.2259060.22162390.9620.9681000.185
1.613-1.6590.2222750.20558260.20661010.9670.9731000.173
1.659-1.710.2363200.19156220.19359420.9670.9761000.159
1.71-1.7660.2212830.17854660.1857500.970.9899.98260.148
1.766-1.8280.1952650.16652880.16755530.9760.9831000.139
1.828-1.8970.1892440.16351440.16453880.9770.9831000.138
1.897-1.9750.1892480.15749260.15851740.9770.9851000.134
1.975-2.0620.1652620.15247330.15349950.9810.9861000.132
2.062-2.1630.1612210.14545320.14647530.9850.9871000.129
2.163-2.2790.1742440.14443090.14645530.9830.9871000.129
2.279-2.4170.1642150.13940970.1443120.9830.9881000.127
2.417-2.5840.1682100.14238350.14340450.9830.9881000.13
2.584-2.790.1612070.14535950.14638030.9830.98799.97370.138
2.79-3.0550.1531940.14632890.14734830.9850.9871000.141
3.055-3.4140.1521590.14730210.14831800.9850.9871000.15
3.414-3.9390.1621330.14827080.14928430.9840.98799.92970.157
3.939-4.8160.1461200.14122920.14224120.9890.9881000.156
4.816-6.7760.218850.1918240.19119090.9770.9851000.204
6.776-47.6280.178520.19110880.1911410.9860.98299.91240.212

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