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- PDB-9xpr: Maltose-binding protein -

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Basic information

Entry
Database: PDB / ID: 9xpr
TitleMaltose-binding protein
Componentsmaltose-binding protein
KeywordsSUGAR BINDING PROTEIN / maltose-binding protein
Function / homologybeta-maltotriose
Function and homology information
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsItoh, T. / Hibi, T. / Kimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05494 Japan
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural characterization of an alpha-glucosaccharide-binding protein from Paenibacillus sp. str. FPU-7.
Authors: Itoh, T. / Kataoka, K. / Kaneko, Y. / Hibi, T. / Kimoto, H.
History
DepositionNov 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 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: maltose-binding protein
B: maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9534
Polymers89,9442
Non-polymers1,0092
Water11,692649
1
A: maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4762
Polymers44,9721
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4762
Polymers44,9721
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.443, 64.765, 82.507
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein maltose-binding protein


Mass: 44971.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DDBJ:LC899132 / Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.5 Å / Num. obs: 96832 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.027 / Net I/σ(I): 19.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4579 / CC1/2: 0.779 / Rpim(I) all: 0.49 / Rrim(I) all: 0.794 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.6→33.52 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 4723 4.88 %
Rwork0.192 --
obs0.1939 96779 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6208 0 68 649 6925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066531
X-RAY DIFFRACTIONf_angle_d0.8258865
X-RAY DIFFRACTIONf_dihedral_angle_d16.4612479
X-RAY DIFFRACTIONf_chiral_restr0.05967
X-RAY DIFFRACTIONf_plane_restr0.0061138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33171430.28382919X-RAY DIFFRACTION95
1.62-1.640.32881520.28023051X-RAY DIFFRACTION100
1.64-1.660.29931450.2633045X-RAY DIFFRACTION100
1.66-1.680.29281510.26383080X-RAY DIFFRACTION100
1.68-1.70.29921600.26233055X-RAY DIFFRACTION100
1.7-1.720.31061430.26213092X-RAY DIFFRACTION100
1.72-1.750.30071580.25793071X-RAY DIFFRACTION100
1.75-1.770.2861520.2483058X-RAY DIFFRACTION100
1.77-1.80.31471630.24053077X-RAY DIFFRACTION100
1.8-1.830.26871370.24763051X-RAY DIFFRACTION100
1.83-1.860.29431680.24563040X-RAY DIFFRACTION100
1.86-1.90.31231640.24963064X-RAY DIFFRACTION100
1.9-1.930.29221440.24923072X-RAY DIFFRACTION100
1.93-1.970.26091510.23713094X-RAY DIFFRACTION100
1.97-2.020.28461670.23513085X-RAY DIFFRACTION100
2.02-2.060.26121420.23213082X-RAY DIFFRACTION100
2.06-2.110.26681600.22613043X-RAY DIFFRACTION100
2.11-2.170.2671600.2213070X-RAY DIFFRACTION100
2.17-2.240.29661540.22953067X-RAY DIFFRACTION99
2.24-2.310.24641560.2213034X-RAY DIFFRACTION99
2.31-2.390.26551750.2223054X-RAY DIFFRACTION100
2.39-2.490.2711650.223075X-RAY DIFFRACTION100
2.49-2.60.25071690.2163066X-RAY DIFFRACTION100
2.6-2.740.25421560.20443094X-RAY DIFFRACTION100
2.74-2.910.24321490.19713089X-RAY DIFFRACTION100
2.91-3.130.21841880.19523041X-RAY DIFFRACTION100
3.13-3.450.22771700.17833100X-RAY DIFFRACTION100
3.45-3.940.18521610.15583108X-RAY DIFFRACTION100
3.94-4.960.17521460.13153134X-RAY DIFFRACTION100
4.97-33.520.17191740.14993145X-RAY DIFFRACTION99

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