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- PDB-22hj: Beta-1,2-glucan-binding protein soaked with cyclic beta-1,2-gluco... -

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Basic information

Entry
Database: PDB / ID: 22hj
TitleBeta-1,2-glucan-binding protein soaked with cyclic beta-1,2-glucooctaose
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
Extracellular solute-binding protein family 1
Similarity search - Component
Biological speciesChloroflexus aurantiacus Y-400-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHirayama, R. / Nakajima, M.
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)55,52911
Polymers53,0531
Non-polymers2,47610
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.699, 82.849, 94.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, bis-Tris, cyclic beta-1,2-glucooctaose

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.25 Å / Num. obs: 75627 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 1 / Net I/σ(I): 33.9
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 3708 / CC1/2: 0.946 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.992 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1813 3838 5.082 %
Rwork0.1668 71687 -
all0.168 --
obs-75525 99.938 %
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: 20.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.014 Å2-0 Å20 Å2
2---0.005 Å2-0 Å2
3----0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 163 302 3840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123697
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163349
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.85033
X-RAY DIFFRACTIONr_angle_other_deg1.0421.7387724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.064517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75610562
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.03710181
X-RAY DIFFRACTIONr_chiral_restr0.1020.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024337
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02869
X-RAY DIFFRACTIONr_nbd_refined0.3250.2813
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23140
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21837
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.215
X-RAY DIFFRACTIONr_nbd_other0.2140.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.217
X-RAY DIFFRACTIONr_mcbond_it1.9811.9531726
X-RAY DIFFRACTIONr_mcbond_other1.9811.9531726
X-RAY DIFFRACTIONr_mcangle_it2.6223.5072168
X-RAY DIFFRACTIONr_mcangle_other2.6273.5082169
X-RAY DIFFRACTIONr_scbond_it3.5862.3121971
X-RAY DIFFRACTIONr_scbond_other3.5352.2991964
X-RAY DIFFRACTIONr_scangle_it5.2594.0852865
X-RAY DIFFRACTIONr_scangle_other5.1694.0622854
X-RAY DIFFRACTIONr_lrange_it5.65521.6924320
X-RAY DIFFRACTIONr_lrange_other5.65521.694320
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
1.6-1.6410.2382630.21452460.21555100.9610.96999.98180.171
1.641-1.6860.2132610.21251180.21253800.9710.96799.98140.167
1.686-1.7350.2222750.19449210.19551980.970.97699.96150.152
1.735-1.7880.2182630.1948390.19251030.9710.97499.98040.151
1.788-1.8470.2132460.18946810.1949320.9730.97599.89860.151
1.847-1.9120.2112370.17845180.1847590.9720.9899.9160.141
1.912-1.9840.1872050.17444220.17546310.9790.98199.91360.136
1.984-2.0640.2022390.16642100.16844510.9740.98399.95510.136
2.064-2.1560.2062280.16440350.16642630.9750.9831000.135
2.156-2.2610.1561870.15439080.15540950.9840.9851000.131
2.261-2.3820.1781990.15736800.15838820.9810.98599.92270.135
2.382-2.5260.1631800.15135160.15237000.9830.98699.89190.132
2.526-2.70.1631870.15533140.15635040.9820.98599.91440.137
2.7-2.9140.1751780.16130720.16132520.980.98499.93850.147
2.914-3.1910.1881700.16628290.16730000.9770.98399.96670.156
3.191-3.5640.1711610.16125660.16227270.9830.9841000.159
3.564-4.1080.1561130.15323300.15324430.9850.9861000.157
4.108-5.0150.1391040.14619770.14620810.9910.9881000.153
5.015-7.0250.179920.19315620.19216540.9840.9821000.198
7.025-35.9920.286500.1989430.2019970.9620.97999.59880.209

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