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

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Basic information

Entry
Database: PDB / ID: 5mtt
TitleMaltodextrin binding protein MalE1 from L. casei BL23 bound to maltotetraose
ComponentsMalE1
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein / lactobacillus casei
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
alpha-maltotetraose / alpha-D-glucopyranose / MalE1
Similarity search - Component
Biological speciesLactobacillus casei BL23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.12 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
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)42,68120
Polymers40,5051
Non-polymers2,17619
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint38 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.494, 83.079, 85.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MalE1 / periplasmic maltodextrin binding protein MalE1


Mass: 40504.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei BL23 (bacteria) / Gene: malE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0L7B0

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Sugars , 2 types, 5 molecules

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


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 468 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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 / pH: 7
Details: 0.1 mM Na-Hepes, pH 7.0, 20-25% Jeffamine ED2003, pH 7.0, 5 mM maltotetraose, 100 mM LiCl

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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: Mar 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: 1.118→45.28 Å / Num. obs: 146247 / % possible obs: 99.73 % / Redundancy: 11.6 % / Biso Wilson estimate: 12.12 Å2 / CC1/2: 1 / Net I/σ(I): 23.52
Reflection shellResolution: 1.118→1.158 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.1218 / Mean I/σ(I) obs: 2 / Num. unique all: 14158 / CC1/2: 0.742 / Rpim(I) all: 0.386 / % possible all: 97.76

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1168: ???)refinement
XDSVERSION November 11, 2013data reduction
XDSVERSION November 11, 2013data scaling
SHELXDE2013/2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.12→41.54 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 11.82
RfactorNum. reflection% reflectionSelection details
Rfree0.137 7312 5 %random selection
Rwork0.12 ---
obs0.12 146240 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.92 Å2
Refinement stepCycle: LAST / Resolution: 1.12→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 137 454 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093134
X-RAY DIFFRACTIONf_angle_d1.0824254
X-RAY DIFFRACTIONf_dihedral_angle_d12.3131180
X-RAY DIFFRACTIONf_chiral_restr0.085495
X-RAY DIFFRACTIONf_plane_restr0.008532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1179-1.13060.25592250.24774273X-RAY DIFFRACTION93
1.1306-1.14390.22022430.19984619X-RAY DIFFRACTION100
1.1439-1.15780.19812400.18544558X-RAY DIFFRACTION100
1.1578-1.17250.18432410.17984581X-RAY DIFFRACTION100
1.1725-1.18790.18752450.16754660X-RAY DIFFRACTION100
1.1879-1.20420.20492400.16394557X-RAY DIFFRACTION100
1.2042-1.22140.17532440.15564635X-RAY DIFFRACTION100
1.2214-1.23960.17052400.14844548X-RAY DIFFRACTION100
1.2396-1.2590.17642410.13614582X-RAY DIFFRACTION100
1.259-1.27970.16352460.12974668X-RAY DIFFRACTION100
1.2797-1.30170.13762410.12044596X-RAY DIFFRACTION100
1.3017-1.32540.14052410.1164570X-RAY DIFFRACTION100
1.3254-1.35090.15292440.114643X-RAY DIFFRACTION100
1.3509-1.37850.13812420.10454594X-RAY DIFFRACTION100
1.3785-1.40840.13252440.10234634X-RAY DIFFRACTION100
1.4084-1.44120.13852430.09644608X-RAY DIFFRACTION100
1.4412-1.47720.12292420.09114611X-RAY DIFFRACTION100
1.4772-1.51720.11952450.0884642X-RAY DIFFRACTION100
1.5172-1.56180.10712420.08434614X-RAY DIFFRACTION100
1.5618-1.61220.10662450.08024638X-RAY DIFFRACTION100
1.6122-1.66990.11682450.08264664X-RAY DIFFRACTION100
1.6699-1.73670.11082450.08694645X-RAY DIFFRACTION100
1.7367-1.81580.12352420.08994613X-RAY DIFFRACTION100
1.8158-1.91150.11352460.09434671X-RAY DIFFRACTION100
1.9115-2.03130.1152460.09844680X-RAY DIFFRACTION100
2.0313-2.18810.12682470.10274684X-RAY DIFFRACTION100
2.1881-2.40830.11842470.10694692X-RAY DIFFRACTION100
2.4083-2.75670.14112490.12474723X-RAY DIFFRACTION100
2.7567-3.47290.14192500.1394765X-RAY DIFFRACTION100
3.4729-41.56820.14532610.1414960X-RAY DIFFRACTION100

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