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- PDB-6dtu: Maltotetraose bound T. maritima MalE1 -

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Basic information

Entry
Database: PDB / ID: 6dtu
TitleMaltotetraose bound T. maritima MalE1
Componentsmaltose-binding protein MalE1
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / maltose binding protein / maltotetraose
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / proteasome core complex, alpha-subunit complex / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ubiquitin-dependent protein catabolic process
Similarity search - Function
Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / Maltose ABC transporter, periplasmic maltose-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCuneo, M.J. / Shukla, S.
CitationJournal: Biochemistry / Year: 2018
Title: Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics.
Authors: Shukla, S. / Bafna, K. / Gullett, C. / Myles, D.A.A. / Agarwal, P.K. / Cuneo, M.J.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 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 / 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_instance_feature / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: maltose-binding protein MalE1
B: maltose-binding protein MalE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0024
Polymers82,6692
Non-polymers1,3332
Water9,440524
1
A: maltose-binding protein MalE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0012
Polymers41,3341
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein MalE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0012
Polymers41,3341
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.645, 55.465, 93.542
Angle α, β, γ (deg.)96.80, 93.67, 101.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein maltose-binding protein MalE1


Mass: 41334.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1204 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0T1
#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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% poly-ethylene glycol (PEG) 4000, 18% isopropanol and 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 90224 / % possible obs: 83.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.464 / Num. unique obs: 8982

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHA

2gha


Resolution: 1.5→30.816 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.73
RfactorNum. reflection% reflection
Rfree0.2271 1999 2.22 %
Rwork0.2054 --
obs0.2059 90177 83.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→30.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 90 524 6432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076174
X-RAY DIFFRACTIONf_angle_d0.9688411
X-RAY DIFFRACTIONf_dihedral_angle_d15.1842280
X-RAY DIFFRACTIONf_chiral_restr0.086947
X-RAY DIFFRACTIONf_plane_restr0.0071086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53440.31821340.30425925X-RAY DIFFRACTION78
1.5344-1.57590.23991460.24266419X-RAY DIFFRACTION84
1.5759-1.62230.30841430.2236321X-RAY DIFFRACTION84
1.6223-1.67460.23341450.20836370X-RAY DIFFRACTION84
1.6746-1.73450.25611470.20016468X-RAY DIFFRACTION84
1.7345-1.80390.25061430.20776330X-RAY DIFFRACTION84
1.8039-1.8860.26481390.21236120X-RAY DIFFRACTION81
1.886-1.98540.23431350.21825937X-RAY DIFFRACTION78
1.9854-2.10980.21341320.20295858X-RAY DIFFRACTION78
2.1098-2.27260.22661320.20265788X-RAY DIFFRACTION76
2.2726-2.50120.22451440.2116411X-RAY DIFFRACTION84
2.5012-2.86290.25221550.22136812X-RAY DIFFRACTION90
2.8629-3.60610.23491550.20436881X-RAY DIFFRACTION91
3.6061-100.17681490.17886538X-RAY DIFFRACTION86

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