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- PDB-6dtt: Apo T. maritima MalE2 -

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Basic information

Entry
Database: PDB / ID: 6dtt
TitleApo T. maritima MalE2
Componentsmaltose-binding protein MalE2
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
Maltose ABC transporter, periplasmic maltose-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Shukla, S.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: T. maritima MalE2 apo
Authors: Cuneo, M.J. / Shukla, S.
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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maltose-binding protein MalE2
B: maltose-binding protein MalE2


Theoretical massNumber of molelcules
Total (without water)84,1262
Polymers84,1262
Non-polymers00
Water7,008389
1
A: maltose-binding protein MalE2


Theoretical massNumber of molelcules
Total (without water)42,0631
Polymers42,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein MalE2


Theoretical massNumber of molelcules
Total (without water)42,0631
Polymers42,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.922, 91.019, 100.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:7 or resseq 9:34 or resseq...
21(chain B and (resseq 5:7 or resseq 9:34 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 5:7 or resseq 9:34 or resseq...A5 - 7
121(chain A and (resseq 5:7 or resseq 9:34 or resseq...A9 - 34
131(chain A and (resseq 5:7 or resseq 9:34 or resseq...A36 - 42
141(chain A and (resseq 5:7 or resseq 9:34 or resseq...A5 - 90
151(chain A and (resseq 5:7 or resseq 9:34 or resseq...A5 - 377
161(chain A and (resseq 5:7 or resseq 9:34 or resseq...A5 - 377
171(chain A and (resseq 5:7 or resseq 9:34 or resseq...A5 - 377
181(chain A and (resseq 5:7 or resseq 9:34 or resseq...A142 - 199
191(chain A and (resseq 5:7 or resseq 9:34 or resseq...A238 - 291
1101(chain A and (resseq 5:7 or resseq 9:34 or resseq...A293 - 302
1111(chain A and (resseq 5:7 or resseq 9:34 or resseq...A304 - 314
1121(chain A and (resseq 5:7 or resseq 9:34 or resseq...A316 - 328
1131(chain A and (resseq 5:7 or resseq 9:34 or resseq...A330 - 343
1141(chain A and (resseq 5:7 or resseq 9:34 or resseq...A345 - 350
1151(chain A and (resseq 5:7 or resseq 9:34 or resseq...A352 - 35375
1161(chain A and (resseq 5:7 or resseq 9:34 or resseq...A37764
1171(chain A and (resseq 5:7 or resseq 9:34 or resseq...A366 - 375
1181(chain A and (resseq 5:7 or resseq 9:34 or resseq...A377
211(chain B and (resseq 5:7 or resseq 9:34 or resseq...B5 - 7
221(chain B and (resseq 5:7 or resseq 9:34 or resseq...B9 - 34
231(chain B and (resseq 5:7 or resseq 9:34 or resseq...B36 - 42
241(chain B and (resseq 5:7 or resseq 9:34 or resseq...B85 - 90
251(chain B and (resseq 5:7 or resseq 9:34 or resseq...B3
261(chain B and (resseq 5:7 or resseq 9:34 or resseq...B4 - 377
271(chain B and (resseq 5:7 or resseq 9:34 or resseq...B4 - 377
281(chain B and (resseq 5:7 or resseq 9:34 or resseq...B142 - 199
291(chain B and (resseq 5:7 or resseq 9:34 or resseq...B4 - 377
2101(chain B and (resseq 5:7 or resseq 9:34 or resseq...B238 - 2933
2111(chain B and (resseq 5:7 or resseq 9:34 or resseq...B316 - 32314
2121(chain B and (resseq 5:7 or resseq 9:34 or resseq...B316 - 328
2131(chain B and (resseq 5:7 or resseq 9:34 or resseq...B330 - 343
2141(chain B and (resseq 5:7 or resseq 9:34 or resseq...B358 - 36356
2151(chain B and (resseq 5:7 or resseq 9:34 or resseq...B358 - 364
2161(chain B and (resseq 5:7 or resseq 9:34 or resseq...B366 - 375
2171(chain B and (resseq 5:7 or resseq 9:34 or resseq...B377

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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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1839 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S5Y1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 7.5 / Details: 26% PEG 3350 and 0.1M sodium di-phosphate

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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: 1.9→30 Å / Num. obs: 55922 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 2.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.472 / Num. unique obs: 5603

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FNC

2fnc


Resolution: 1.9→29.814 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2337 2000 3.58 %
Rwork0.1926 --
obs0.1941 55874 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.11 Å2 / Biso mean: 28.8801 Å2 / Biso min: 14.82 Å2
Refinement stepCycle: final / Resolution: 1.9→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 0 389 6144
Biso mean---33.45 -
Num. residues----747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065997
X-RAY DIFFRACTIONf_angle_d0.828145
X-RAY DIFFRACTIONf_chiral_restr0.053891
X-RAY DIFFRACTIONf_plane_restr0.0051062
X-RAY DIFFRACTIONf_dihedral_angle_d14.5523613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3156X-RAY DIFFRACTION6.343TORSIONAL
12B3156X-RAY DIFFRACTION6.343TORSIONAL
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 (%)
1.8996-1.94710.33131400.27963786392697
1.9471-1.99980.31771430.24243841398498
1.9998-2.05860.25161430.2313849399298
2.0586-2.1250.26751420.22193830397298
2.125-2.20090.27871430.20853864400798
2.2009-2.2890.23791430.20323838398198
2.289-2.39320.26111450.20363892403798
2.3932-2.51930.24921430.20113847399098
2.5193-2.6770.28191430.20343871401498
2.677-2.88360.25371440.21763880402498
2.8836-3.17340.22841430.21263854399797
3.1734-3.6320.22131430.19593840398396
3.632-4.57320.20841420.1543826396895
4.5732-29.81760.18361430.15513856399992

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