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- PDB-7ffw: The crystal structure of a domain-swapped dimeric maltodextrin-bi... -

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Basic information

Entry
Database: PDB / ID: 7ffw
TitleThe crystal structure of a domain-swapped dimeric maltodextrin-binding protein MalE from Salmonella enterica
ComponentsMaltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / domain-swapped / maltodextrin-binding protein / MalE / HYDROLASE
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
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
alpha-maltopentaose / METHOXYETHANE / Maltodextrin-binding protein
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWang, L. / Bu, T. / Bai, X.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029736 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structure of the domain-swapped dimeric maltodextrin-binding protein MalE from Salmonella enterica.
Authors: Wang, L. / Bu, T. / Bai, X. / He, S. / Zhang, J. / Jin, L. / Liu, B. / Dong, Y. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8326
Polymers40,6411
Non-polymers1,1915
Water6,251347
1
A: Maltodextrin-binding protein
hetero molecules

A: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,66512
Polymers81,2822
Non-polymers2,38210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area29290 Å2
ΔGint-141 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.714, 89.692, 64.066
Angle α, β, γ (deg.)90.000, 114.766, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltodextrin-binding protein


Mass: 40641.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: malE, AL463_06150, EDJ01_24875 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0W3SG76
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 351 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-2ME / METHOXYETHANE


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.1 M Ammonium sulfate, 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate, pH5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→39.82 Å / Num. obs: 58520 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.75 Å2 / Rsym value: 0.062 / Net I/σ(I): 33.2889
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 4766 / Rsym value: 0.492

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→39.82 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 1997 3.42 %
Rwork0.1819 56408 -
obs0.1827 58405 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 80 347 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883055
X-RAY DIFFRACTIONf_angle_d1.0424156
X-RAY DIFFRACTIONf_chiral_restr0.0585462
X-RAY DIFFRACTIONf_plane_restr0.0063530
X-RAY DIFFRACTIONf_dihedral_angle_d7.12212467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.46211210.42453419X-RAY DIFFRACTION84.17
1.64-1.680.34681420.38244000X-RAY DIFFRACTION97.8
1.68-1.730.33591430.33434039X-RAY DIFFRACTION99.22
1.73-1.790.33391450.28744063X-RAY DIFFRACTION99.57
1.79-1.850.27961420.25324033X-RAY DIFFRACTION99.67
1.85-1.930.27351450.22674085X-RAY DIFFRACTION99.62
1.93-2.020.24131450.19364079X-RAY DIFFRACTION99.93
2.02-2.120.20311430.17734073X-RAY DIFFRACTION99.72
2.12-2.250.17481440.16374064X-RAY DIFFRACTION99.64
2.25-2.430.22881460.17224103X-RAY DIFFRACTION99.91
2.43-2.670.20531450.16244086X-RAY DIFFRACTION99.91
2.67-3.060.18071450.16024089X-RAY DIFFRACTION99.91
3.06-3.850.17411440.1494095X-RAY DIFFRACTION99.65
3.85-39.820.171470.15694180X-RAY DIFFRACTION99.91

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