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- PDB-6dts: Maltotetraose bound T. maritima MalE2 -

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Basic information

Entry
Database: PDB / ID: 6dts
TitleMaltotetraose bound T. maritima MalE2
Componentsmaltose-binding protein MalE2
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / maltose binding protein / maltotetraose
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 / proteasome core complex, alpha-subunit complex / 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 MalE2
B: maltose-binding protein MalE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4604
Polymers84,1262
Non-polymers1,3332
Water13,151730
1
A: maltose-binding protein MalE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7302
Polymers42,0631
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein MalE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7302
Polymers42,0631
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.441, 56.123, 88.322
Angle α, β, γ (deg.)89.580, 84.630, 89.670
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 16 or resid 18...
21(chain B and (resid 5 through 16 or resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 16 or resid 18...A5 - 16
121(chain A and (resid 5 through 16 or resid 18...A18 - 24
131(chain A and (resid 5 through 16 or resid 18...A26 - 39
141(chain A and (resid 5 through 16 or resid 18...A87 - 91
151(chain A and (resid 5 through 16 or resid 18...A93 - 214
161(chain A and (resid 5 through 16 or resid 18...A216 - 217
171(chain A and (resid 5 through 16 or resid 18...A219 - 343
181(chain A and (resid 5 through 16 or resid 18...A345 - 382
191(chain A and (resid 5 through 16 or resid 18...A460
211(chain B and (resid 5 through 16 or resid 18...B5 - 16
221(chain B and (resid 5 through 16 or resid 18...B18 - 24
231(chain B and (resid 5 through 16 or resid 18...B26 - 39
241(chain B and (resid 5 through 16 or resid 18...B41 - 85
251(chain B and (resid 5 through 16 or resid 18...B93 - 214
261(chain B and (resid 5 through 16 or resid 18...B5 - 460
271(chain B and (resid 5 through 16 or resid 18...B219 - 343
281(chain B and (resid 5 through 16 or resid 18...B5 - 460
291(chain B and (resid 5 through 16 or resid 18...B345 - 460

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Components

#1: Protein maltose-binding protein MalE2


Mass: 42063.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1839 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S5Y1
#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 / Water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% PEG 3350, 0.3M sodium acetate and 0.1M bis-Tris pH 5.5

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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 1, 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: 98262 / % possible obs: 90.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 7.1
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.125 / Num. unique obs: 7822

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FNC

2fnc


Resolution: 1.5→31.737 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 18.22
RfactorNum. reflection% reflection
Rfree0.1907 1969 2 %
Rwork0.1692 --
obs0.1696 98260 90.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.48 Å2 / Biso mean: 22.0064 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 1.5→31.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5836 0 90 730 6656
Biso mean--17.07 29.45 -
Num. residues----757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2176X-RAY DIFFRACTION0.976TORSIONAL
12B2176X-RAY DIFFRACTION0.976TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.498-1.53540.22531330.20316378651183
1.5354-1.57690.23991360.18016548668486
1.5769-1.62330.19461400.16826647678787
1.6233-1.67570.21521360.15936669680588
1.6757-1.73560.21711350.15886769690488
1.7356-1.80510.18731420.16376818696089
1.8051-1.88730.1981410.17216880702190
1.8873-1.98670.18711360.16616925706191
1.9867-2.11120.20351510.17377023717492
2.1112-2.27420.21781460.16887047719392
2.2742-2.50290.20191500.17497162731294
2.5029-2.86490.20151450.18637181732694
2.8649-3.60870.19991420.17597140728293
3.6087-31.74440.14711360.15197104724093

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