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- PDB-6l0z: The crystal structure of Salmonella enterica sugar-binding protei... -

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Basic information

Entry
Database: PDB / ID: 6l0z
TitleThe crystal structure of Salmonella enterica sugar-binding protein MalE
ComponentsMaltodextrin-binding protein
KeywordsSUGAR BINDING PROTEIN / Salmonella enterica / MalE / sugar-binding protein
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / 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-maltose / METHOXYETHANE / 1,5-anhydro-D-glucitol / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWang, L. / Chen, Y. / Liu, W. / Lan, J. / Shang, F. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: To Be Published
Title: The crystal structure of Salmonella enterica sugar-binding protein MalE
Authors: Wang, L. / Chen, Y. / Liu, W. / Lan, J. / Shang, F. / Xu, Y.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,33617
Polymers40,6411
Non-polymers1,69516
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area15220 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

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Components

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Protein , 1 types, 1 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, UniProt: P19576*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-ASO / 1,5-anhydro-D-glucitol / 1,5-ANHYDROSORBITOL / 1,5-Anhydroglucitol


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
D-1-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 406 molecules

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


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


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 50% MPD, 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: 1.6→50 Å / Num. obs: 58520 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.09 Å2 / Rsym value: 0.112 / Net I/σ(I): 33.29
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 273 / Rsym value: 0.112

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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: 0.1612 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1805 1999 3.42 %
Rwork0.1567 56474 -
obs0.1575 58473 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 111 394 3334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01153052
X-RAY DIFFRACTIONf_angle_d1.44444140
X-RAY DIFFRACTIONf_chiral_restr0.0596457
X-RAY DIFFRACTIONf_plane_restr0.007525
X-RAY DIFFRACTIONf_dihedral_angle_d7.29832469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32571220.2743445X-RAY DIFFRACTION84.81
1.64-1.680.23381420.24444017X-RAY DIFFRACTION98.21
1.68-1.730.23961440.21594049X-RAY DIFFRACTION99.48
1.73-1.790.19061450.19464066X-RAY DIFFRACTION99.65
1.79-1.850.22491420.17984033X-RAY DIFFRACTION99.67
1.85-1.930.2211450.17844094X-RAY DIFFRACTION99.84
1.93-2.020.20591450.16484080X-RAY DIFFRACTION99.95
2.02-2.120.18961430.15344073X-RAY DIFFRACTION99.72
2.12-2.250.17711440.14354064X-RAY DIFFRACTION99.64
2.25-2.430.19281460.14934103X-RAY DIFFRACTION99.91
2.43-2.670.1841450.1454086X-RAY DIFFRACTION99.91
2.67-3.060.17061450.14784089X-RAY DIFFRACTION99.91
3.06-3.850.16991440.1374095X-RAY DIFFRACTION99.65
3.85-39.820.1521470.15344180X-RAY DIFFRACTION99.91

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