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- PDB-9kha: Crystal structure of maltodextrin-binding protein SPs0871 from St... -

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Basic information

Entry
Database: PDB / ID: 9kha
TitleCrystal structure of maltodextrin-binding protein SPs0871 from Streptococcus pyogenes at 2.20 A
ComponentsExtracellular solute-binding protein
KeywordsSUGAR BINDING PROTEIN / Streptococcus pyogenes / virtual screening / biophysical-based screening / small compounds
Function / homologyBacterial extracellular solute-binding protein / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Extracellular solute-binding protein
Function and homology information
Biological speciesStreptococcus pyogenes M1 GAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCaaveiro, J.M.M. / Yamawaki, T. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Rep / Year: 2025
Title: Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings.
Authors: Yamawaki, T. / Nakakido, M. / Nagatoishi, S. / Caaveiro, J.M.M. / Kuroda, D. / Aikawa, C. / Nakagawa, I. / Tsumoto, K.
History
DepositionNov 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: 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
B: Extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)83,9962
Polymers83,9962
Non-polymers00
Water5,585310
1
A: Extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)41,9981
Polymers41,9981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)41,9981
Polymers41,9981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.189, 118.189, 353.944
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 39 - 413 / Label seq-ID: 13 - 387

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Extracellular solute-binding protein


Mass: 41997.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes M1 GAS (bacteria)
Gene: E0F66_03780 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5S4U0C2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293.13 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Ammonium citrate tribasic 1.8 M

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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 S 6M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.3 Å / Num. obs: 47995 / % possible obs: 98.4 % / Redundancy: 17.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.02 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 6775 / CC1/2: 0.985 / Rpim(I) all: 0.098 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.58 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.182
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2237 2392 4.984 %
Rwork0.1849 45602 -
all0.187 --
obs-47994 98.427 %
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: 40.898 Å2
Baniso -1Baniso -2Baniso -3
1-1.516 Å20.758 Å20 Å2
2--1.516 Å20 Å2
3----4.918 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 0 310 5935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165429
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.8087779
X-RAY DIFFRACTIONr_angle_other_deg0.4941.76412573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.82154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36310999
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.41110242
X-RAY DIFFRACTIONr_chiral_restr0.070.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
X-RAY DIFFRACTIONr_nbd_refined0.2170.21180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24743
X-RAY DIFFRACTIONr_nbtor_refined0.180.22939
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.29
X-RAY DIFFRACTIONr_nbd_other0.1740.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.214
X-RAY DIFFRACTIONr_mcbond_it1.8542.7922955
X-RAY DIFFRACTIONr_mcbond_other1.8522.7922955
X-RAY DIFFRACTIONr_mcangle_it2.695.0113690
X-RAY DIFFRACTIONr_mcangle_other2.695.0123691
X-RAY DIFFRACTIONr_scbond_it2.8053.1282794
X-RAY DIFFRACTIONr_scbond_other2.8043.1292795
X-RAY DIFFRACTIONr_scangle_it4.4675.5834086
X-RAY DIFFRACTIONr_scangle_other4.4675.5834087
X-RAY DIFFRACTIONr_lrange_it5.55827.0296622
X-RAY DIFFRACTIONr_lrange_other5.54126.886562
X-RAY DIFFRACTIONr_ncsr_local_group_10.0750.0511851
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.075140.05009
12AX-RAY DIFFRACTIONLocal ncs0.075140.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.271320.2392852X-RAY DIFFRACTION84.6285
2.257-2.3190.2221630.2093111X-RAY DIFFRACTION93.9724
2.319-2.3860.2081890.1913168X-RAY DIFFRACTION99.881
2.386-2.4590.241750.1753117X-RAY DIFFRACTION100
2.459-2.5390.2431500.1973021X-RAY DIFFRACTION100
2.539-2.6280.2461740.1972918X-RAY DIFFRACTION100
2.628-2.7270.231480.1952835X-RAY DIFFRACTION100
2.727-2.8380.2471320.1962722X-RAY DIFFRACTION100
2.838-2.9640.2581420.1932629X-RAY DIFFRACTION100
2.964-3.1080.2541220.2042512X-RAY DIFFRACTION100
3.108-3.2750.2271350.1972374X-RAY DIFFRACTION100
3.275-3.4720.231290.1912254X-RAY DIFFRACTION100
3.472-3.7110.213930.1782145X-RAY DIFFRACTION100
3.711-4.0060.2261040.1662009X-RAY DIFFRACTION100
4.006-4.3840.165950.1431835X-RAY DIFFRACTION100
4.384-4.8960.183760.1491694X-RAY DIFFRACTION100
4.896-5.6430.187800.171487X-RAY DIFFRACTION100
5.643-6.8840.237710.1911274X-RAY DIFFRACTION99.9257
6.884-9.6260.258520.1811017X-RAY DIFFRACTION100
9.626-45.30.227300.245628X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.95140.3909-0.56631.0026-0.58531.341-0.05990.21140.1531-0.09030.04610.0502-0.0986-0.09110.01380.041-0.0123-0.03550.04980.0320.073-7.3913-43.5252-2.5532
20.98360.1327-0.79490.5518-0.20291.88280.0944-0.07050.15520.1968-0.06740.1231-0.3314-0.2328-0.02710.16820.03870.01360.0877-0.04820.0904-17.3051-49.539256.0906
Refinement TLS groupSelection: ALL

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