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- PDB-21dh: Crystal structure of MBP-fused Monobody P' in complex with HPPU -

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Basic information

Entry
Database: PDB / ID: 21dh
TitleCrystal structure of MBP-fused Monobody P' in complex with HPPU
ComponentsMaltose/maltodextrin-binding periplasmic protein,Monobody P'
KeywordsCELL ADHESION / engineered binding protein / fibronectin type III domain / ligand-binding complex / beta-sandwich fold
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
beta-maltose / : / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsEndo, K. / Umemoto, S. / Okumura, H. / Sato, Y. / Tsukiji, S. / Nagano, S. / Murakami, H. / Hino, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04753 Japan
Japan Society for the Promotion of Science (JSPS)23H05456 Japan
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystallization and X-ray structure of a highly aggregation-prone monobody engineered for high-affinity small-molecule recognition.
Authors: Endo, K. / Umemoto, S. / Tsuzuki, N. / Okumura, H. / Sato, Y. / Yoshii, T. / Tsukiji, S. / Nagano, S. / Murakami, H. / Hino, T.
#1: Journal: To Be Published
Title: Crystallization and X-ray structure of a highly aggregation-prone monobody engineered for high-affinity small-molecule recognition
Authors: Endo, K. / Umemoto, S. / Tsuzuki, N. / Okumura, H. / Sato, Y. / Yoshii, T. / Tsukiji, S. / Nagano, S. / Murakami, H. / Hino, T.
History
DepositionDec 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 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/maltodextrin-binding periplasmic protein,Monobody P'
B: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
C: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
D: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
E: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
F: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,83218
Polymers323,4096
Non-polymers3,42312
Water3,567198
1
A: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Maltose/maltodextrin-binding periplasmic protein,Monobody P'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4723
Polymers53,9011
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.159, 170.581, 422.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody
Maltose/maltodextrin-binding periplasmic protein,Monobody P' / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 53901.496 Da / Num. of mol.: 6 / Mutation: A324V
Source method: isolated from a genetically manipulated source
Details: N-terminal MBP fused Monobody P'
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) synthetic construct (others)
Gene: malE, b4034, JW3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-A1MC1 / 1-(4-hydroxyphenyl)-3-phenyl-urea


Mass: 228.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 4000, 0.1M sodium acetate, 0.28M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→49.33 Å / Num. obs: 113710 / % possible obs: 99.7 % / Redundancy: 6.93 % / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / Net I/σ(I): 10.32
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 5.46 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21765 / CC1/2: 0.548 / Rpim(I) all: 0.571 / Rrim(I) all: 1.359 / % possible all: 98.36

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→49.33 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 5597 4.92 %
Rwork0.2133 --
obs0.215 113710 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21604 0 240 198 22042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222425
X-RAY DIFFRACTIONf_angle_d0.50930556
X-RAY DIFFRACTIONf_dihedral_angle_d14.4178116
X-RAY DIFFRACTIONf_chiral_restr0.0423338
X-RAY DIFFRACTIONf_plane_restr0.0033913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.60.47791550.44513425X-RAY DIFFRACTION93
2.6-2.630.44761820.38723446X-RAY DIFFRACTION98
2.63-2.660.4271690.35253623X-RAY DIFFRACTION100
2.66-2.690.37741620.31723584X-RAY DIFFRACTION100
2.69-2.730.30842070.28043569X-RAY DIFFRACTION100
2.73-2.770.34651560.27093583X-RAY DIFFRACTION100
2.77-2.810.26711850.25343617X-RAY DIFFRACTION100
2.81-2.850.29551900.25643565X-RAY DIFFRACTION100
2.85-2.890.32371820.25793592X-RAY DIFFRACTION100
2.89-2.940.3112310.263516X-RAY DIFFRACTION100
2.94-2.990.28122040.26033618X-RAY DIFFRACTION100
2.99-3.050.31311830.28453532X-RAY DIFFRACTION100
3.05-3.10.31181430.29183681X-RAY DIFFRACTION100
3.1-3.170.31562040.27653537X-RAY DIFFRACTION100
3.17-3.240.30381940.26383565X-RAY DIFFRACTION100
3.24-3.310.30721910.2553628X-RAY DIFFRACTION100
3.31-3.40.2671930.24023578X-RAY DIFFRACTION100
3.4-3.490.28441760.23413588X-RAY DIFFRACTION100
3.49-3.590.28721690.22833620X-RAY DIFFRACTION100
3.59-3.710.27041880.22353624X-RAY DIFFRACTION100
3.71-3.840.25571760.21983613X-RAY DIFFRACTION100
3.84-3.990.23751890.20343617X-RAY DIFFRACTION100
3.99-4.170.21622100.1873595X-RAY DIFFRACTION100
4.17-4.390.20462060.17573605X-RAY DIFFRACTION100
4.39-4.670.20761890.16863649X-RAY DIFFRACTION100
4.67-5.030.18862040.16473639X-RAY DIFFRACTION100
5.03-5.530.21151760.17923683X-RAY DIFFRACTION100
5.53-6.330.25822150.20743624X-RAY DIFFRACTION100
6.33-7.970.20661860.18853715X-RAY DIFFRACTION100
7.97-49.330.17831820.16243882X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -32.7018 Å / Origin y: -18.9942 Å / Origin z: 51.3887 Å
111213212223313233
T0.3605 Å2-0.0223 Å20.0457 Å2-0.3455 Å20.0202 Å2--0.5327 Å2
L0.3446 °2-0.0044 °2-0.0846 °2-0.237 °2-0.0753 °2--0.5615 °2
S0.0062 Å °-0.0978 Å °-0.0093 Å °0.0313 Å °0.0452 Å °0.0233 Å °-0.0156 Å °0.0194 Å °-0.05 Å °
Refinement TLS groupSelection details: all

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