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

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Basic information

Entry
Database: PDB / ID: 7fft
TitleThe crystal structure of a domain-swapped dimeric maltodextrin-binding protein MalE from Salmonella enterica
ComponentsMaltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / maltodextrin-binding protein / MalE / domain-swapped / HYDROLASE
Function / homologyMaltose/Cyclodextrin ABC transporter, substrate-binding protein / carbohydrate transmembrane transporter activity / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / outer membrane-bounded periplasmic space / alpha-maltopentaose / Maltodextrin-binding protein
Function and homology information
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

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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)41,4702
Polymers40,6411
Non-polymers8291
Water4,954275
1
A: Maltodextrin-binding protein
hetero molecules

A: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9404
Polymers81,2822
Non-polymers1,6572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area22480 Å2
ΔGint-166 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.937, 89.406, 64.022
Angle α, β, γ (deg.)90.000, 114.917, 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

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Components

#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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50% (v/v) 2-Methyl-2, 4-pentanediol (MPD) and 0.1 M HEPES (pH 7.5)

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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: 1.599→36.39 Å / Num. obs: 58575 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.61 Å2 / Rsym value: 0.04 / Net I/σ(I): 36.4596
Reflection shellResolution: 1.599→1.656 Å / Num. unique obs: 2661 / Rsym value: 0.221

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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→36.39 Å / SU ML: 0.1388 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 2858 4.88 %
Rwork0.1876 55660 -
obs0.1886 58518 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 56 275 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592961
X-RAY DIFFRACTIONf_angle_d0.84894025
X-RAY DIFFRACTIONf_chiral_restr0.052452
X-RAY DIFFRACTIONf_plane_restr0.0062511
X-RAY DIFFRACTIONf_dihedral_angle_d5.1091735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.24041210.20562273X-RAY DIFFRACTION81.93
1.63-1.660.24521320.20592653X-RAY DIFFRACTION92.62
1.66-1.690.21831280.19522734X-RAY DIFFRACTION96.04
1.69-1.720.24011430.19872789X-RAY DIFFRACTION98.55
1.72-1.760.23911510.1922827X-RAY DIFFRACTION99.43
1.76-1.80.27681440.19252848X-RAY DIFFRACTION99.67
1.8-1.850.26261560.20472822X-RAY DIFFRACTION99.87
1.85-1.90.23281470.20842839X-RAY DIFFRACTION99.9
1.9-1.950.22571350.20712825X-RAY DIFFRACTION99.93
1.95-2.020.25931490.20512836X-RAY DIFFRACTION99.9
2.02-2.090.22661600.20482843X-RAY DIFFRACTION99.97
2.09-2.170.24791410.20182844X-RAY DIFFRACTION99.93
2.17-2.270.20211310.20012849X-RAY DIFFRACTION99.77
2.27-2.390.23691540.20482811X-RAY DIFFRACTION99.9
2.39-2.540.21721400.21072873X-RAY DIFFRACTION99.67
2.54-2.730.24671390.19712828X-RAY DIFFRACTION99.03
2.73-3.010.22491500.19882791X-RAY DIFFRACTION97.16
3.01-3.440.21091500.18612723X-RAY DIFFRACTION96.31
3.44-4.340.13811370.16512798X-RAY DIFFRACTION97.61
4.34-36.390.18081500.16322854X-RAY DIFFRACTION97.63

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