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- PDB-5m28: Maltodextrin binding protein MalE1 from L. casei BL23 bound to ma... -

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Basic information

Entry
Database: PDB / ID: 5m28
TitleMaltodextrin binding protein MalE1 from L. casei BL23 bound to maltotriose
ComponentsMalE1
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein / lactobacillus casei
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. / alpha-maltotriose / MalE1
Function and homology information
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.079 Å
AuthorsHomburg, C. / Bommer, M. / Wuttge, S. / Hobe, C. / Beck, S. / Dobbek, H. / Deutscher, J. / Licht, A. / Schneider, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1078 Germany
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Inducer exclusion in Firmicutes: insights into the regulation of a carbohydrate ATP binding cassette transporter from Lactobacillus casei BL23 by the signal transducing protein P-Ser46-HPr.
Authors: Homburg, C. / Bommer, M. / Wuttge, S. / Hobe, C. / Beck, S. / Dobbek, H. / Deutscher, J. / Licht, A. / Schneider, E.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_audit_support / 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 / struct_conn / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _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.src_method / _entity.type / _pdbx_audit_support.funding_organization
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MalE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6674
Polymers40,0911
Non-polymers5753
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-26 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.273, 82.645, 84.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MalE1 / periplasmic maltodextrin binding protein MalE1


Mass: 40091.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: malE1 / Production host: Escherichia coli (E. coli) / References: UniProt: B0L7B0
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 mM Na-Hepes, pH 7.0, 20-25% Jeffamine ED2003, pH 7.0, 10 mM SrCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2014
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.079→45.73 Å / Num. obs: 155473 / % possible obs: 94.82 % / Observed criterion σ(I): 2 / Redundancy: 16.13 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.3
Reflection shellResolution: 1.079→1.12 Å / Redundancy: 13.36 % / Rmerge(I) obs: 1.102 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.783 / % possible all: 74.32

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1168: ???)refinement
XDSNovember 11, 2013data reduction
XDSNovember 11, 2013data scaling
SHELXDE2013/2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.079→33.443 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.38
RfactorNum. reflection% reflection
Rfree0.1408 7773 5 %
Rwork0.1285 --
obs0.1292 155458 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.079→33.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 36 757 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062968
X-RAY DIFFRACTIONf_angle_d0.9244043
X-RAY DIFFRACTIONf_dihedral_angle_d11.9421089
X-RAY DIFFRACTIONf_chiral_restr0.075463
X-RAY DIFFRACTIONf_plane_restr0.007517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0794-1.09170.27151780.24313387X-RAY DIFFRACTION66
1.0917-1.10460.21722020.19783825X-RAY DIFFRACTION74
1.1046-1.1180.20312240.2014261X-RAY DIFFRACTION83
1.118-1.13220.20942490.18224738X-RAY DIFFRACTION92
1.1322-1.14710.15832550.14314837X-RAY DIFFRACTION94
1.1471-1.16280.15792550.12774851X-RAY DIFFRACTION94
1.1628-1.17940.15942560.12434870X-RAY DIFFRACTION95
1.1794-1.1970.15572590.12284923X-RAY DIFFRACTION96
1.197-1.21570.13452600.13524935X-RAY DIFFRACTION96
1.2157-1.23570.17462590.16624922X-RAY DIFFRACTION95
1.2357-1.2570.15092600.11754930X-RAY DIFFRACTION96
1.257-1.27980.15672610.1214965X-RAY DIFFRACTION96
1.2798-1.30440.21172620.16524980X-RAY DIFFRACTION96
1.3044-1.33110.13652630.12085003X-RAY DIFFRACTION97
1.3311-1.360.13062640.10954999X-RAY DIFFRACTION97
1.36-1.39160.14442640.1145021X-RAY DIFFRACTION97
1.3916-1.42640.13452640.10985014X-RAY DIFFRACTION97
1.4264-1.4650.12842660.11395066X-RAY DIFFRACTION97
1.465-1.50810.12932650.11275022X-RAY DIFFRACTION98
1.5081-1.55680.10922680.10665095X-RAY DIFFRACTION98
1.5568-1.61240.12422670.10365073X-RAY DIFFRACTION98
1.6124-1.6770.11112700.11285132X-RAY DIFFRACTION98
1.677-1.75330.14342690.11515108X-RAY DIFFRACTION98
1.7533-1.84570.1382720.11715167X-RAY DIFFRACTION99
1.8457-1.96140.15182680.13675092X-RAY DIFFRACTION98
1.9614-2.11280.1262740.11225208X-RAY DIFFRACTION99
2.1128-2.32540.14222740.13255200X-RAY DIFFRACTION99
2.3254-2.66170.12532770.12875276X-RAY DIFFRACTION100
2.6617-3.3530.14012800.13185311X-RAY DIFFRACTION100
3.353-33.45930.13362880.13395474X-RAY DIFFRACTION99

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