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- PDB-22hi: Beta-1,2-glucan-binding protein complexed with cyclic beta-1,2-gl... -

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Basic information

Entry
Database: PDB / ID: 22hi
TitleBeta-1,2-glucan-binding protein complexed with cyclic beta-1,2-glucoheptadecaose
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: 1.95 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,9203
Polymers53,0531
Non-polymers2,8672
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.389, 82.908, 94.071
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 Cycloheptadecakis-(1-2)-(beta-D-glucopyranose)


Type: oligosaccharide / Mass: 2774.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,17,17/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a1-q2_a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1_k2-l1_l2-m1_m2-n1_n2-o1_o2-p1_p2-q1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, bis-Tris, cyclic beta-1,2-glucoheptadecaose

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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: 1.95→47.18 Å / Num. obs: 41270 / % possible obs: 98.5 % / Redundancy: 12.4 % / CC1/2: 0.997 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2842 / CC1/2: 0.942 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.176 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2836 1975 4.806 %
Rwork0.2472 39116 -
all0.249 --
obs-41091 97.878 %
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: 31.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20 Å2
2--0.039 Å20 Å2
3---0.032 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 193 104 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123643
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163275
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.8044958
X-RAY DIFFRACTIONr_angle_other_deg0.8291.7357572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.757516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45710540
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.72310177
X-RAY DIFFRACTIONr_chiral_restr0.070.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024183
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02841
X-RAY DIFFRACTIONr_nbd_refined0.3730.2892
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.23202
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21799
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.216
X-RAY DIFFRACTIONr_nbd_other0.2590.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2270.21
X-RAY DIFFRACTIONr_mcbond_it2.3933.0991683
X-RAY DIFFRACTIONr_mcbond_other2.3933.0991683
X-RAY DIFFRACTIONr_mcangle_it3.2545.5672102
X-RAY DIFFRACTIONr_mcangle_other3.2545.5672103
X-RAY DIFFRACTIONr_scbond_it2.7973.381960
X-RAY DIFFRACTIONr_scbond_other2.7963.381961
X-RAY DIFFRACTIONr_scangle_it4.1576.1062856
X-RAY DIFFRACTIONr_scangle_other4.1566.1062857
X-RAY DIFFRACTIONr_lrange_it5.38131.9214257
X-RAY DIFFRACTIONr_lrange_other5.38131.9214258
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
1.95-2.0010.4251380.37828170.3830590.8430.86996.60020.334
2.001-2.0550.2751480.2827730.2830010.9440.94797.33420.238
2.055-2.1150.3081350.26626730.26828810.9420.95197.46620.227
2.115-2.180.3821270.3126080.31428160.8810.89297.12360.27
2.18-2.2510.3831230.32525500.32727350.830.90597.73310.277
2.251-2.330.3691340.29624510.326540.8830.92797.40020.254
2.33-2.4180.2991200.29623770.29625760.8940.92496.93320.256
2.418-2.5160.3271110.27522830.27824500.8950.94497.71430.238
2.516-2.6280.3451120.28422110.28723670.8180.90998.14110.24
2.628-2.7550.3271120.29521120.29722710.9050.89797.93040.25
2.755-2.9040.311950.22820390.23121620.9440.96298.70490.197
2.904-3.0790.317970.28619130.28820500.910.90798.04880.239
3.079-3.2910.329950.27118260.27319500.8910.92998.51280.233
3.291-3.5530.209940.20416740.20517900.9740.97498.7710.19
3.553-3.890.246850.20915710.21116750.9560.9798.86570.2
3.89-4.3460.217730.21414390.21415290.9450.95498.88820.194
4.346-5.0110.173650.18312750.18313560.9810.9798.82010.172
5.011-6.120.281360.22511210.22711650.9160.95999.31330.217
6.12-8.5820.261450.1828770.1859240.9620.98199.78360.181
8.582-47.1760.274300.1925260.1965680.9580.97597.88730.197

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