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- PDB-6dtq: Maltose bound T. maritima MalE3 -

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Basic information

Entry
Database: PDB / ID: 6dtq
TitleMaltose bound T. maritima MalE3
Componentsmaltose-binding protein MalE3
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / maltose binding protein / maltotetraose
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / 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-maltose / TreE / Putative beta-glucosides ABC transporter, substrate binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / Data collection ...Atomic model / 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_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_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 MalE3
B: maltose-binding protein MalE3
C: maltose-binding protein MalE3
D: maltose-binding protein MalE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,23612
Polymers180,7704
Non-polymers1,4668
Water9,260514
1
A: maltose-binding protein MalE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5593
Polymers45,1931
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein MalE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5593
Polymers45,1931
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: maltose-binding protein MalE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5593
Polymers45,1931
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: maltose-binding protein MalE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5593
Polymers45,1931
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.370, 124.034, 174.847
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 19:33 or resseq 35:45 or (resid...
21(chain B and (resseq 19:33 or resseq 35:45 or (resid...
31(chain C and (resseq 19:33 or resseq 35:45 or (resid...
41(chain D and (resseq 19:33 or resseq 35:45 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 33
121(chain A and (resseq 19:33 or resseq 35:45 or (resid...A35 - 45
131(chain A and (resseq 19:33 or resseq 35:45 or (resid...A0
141(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
151(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
161(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
171(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
181(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
191(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
1101(chain A and (resseq 19:33 or resseq 35:45 or (resid...A19 - 502
211(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 33
221(chain B and (resseq 19:33 or resseq 35:45 or (resid...B35 - 45
231(chain B and (resseq 19:33 or resseq 35:45 or (resid...B47
241(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
251(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
261(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
271(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
281(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
291(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
2101(chain B and (resseq 19:33 or resseq 35:45 or (resid...B19 - 502
311(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 33
321(chain C and (resseq 19:33 or resseq 35:45 or (resid...C35 - 45
331(chain C and (resseq 19:33 or resseq 35:45 or (resid...C47
341(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
351(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
361(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
371(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
381(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
391(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
3101(chain C and (resseq 19:33 or resseq 35:45 or (resid...C19 - 502
411(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 33
421(chain D and (resseq 19:33 or resseq 35:45 or (resid...D35 - 45
431(chain D and (resseq 19:33 or resseq 35:45 or (resid...D47
441(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
451(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
461(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
471(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
481(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
491(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502
4101(chain D and (resseq 19:33 or resseq 35:45 or (resid...D19 - 502

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Components

#1: Protein
maltose-binding protein MalE3


Mass: 45192.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Production host: Escherichia coli (E. coli) / References: UniProt: G4FGN8, UniProt: G4XU73*PLUS
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 19% - 25% PEG 3350, 0.4 M sodium thiocynate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 93556 / % possible obs: 95.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.14 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.208 / Net I/σ(I): 9.8 / Num. measured all: 299354
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.232.90.49785751.186188.5
2.23-2.3230.40892741.258195.7
2.32-2.423.10.32993321.265195.7
2.42-2.553.10.26993601.261196.4
2.55-2.713.20.21194691.313196.8
2.71-2.923.20.16394891.317197.1
2.92-3.213.30.11395411.282197.3
3.21-3.683.40.07495441.225196.8
3.68-4.633.40.04995111.111195.6
4.63-403.40.03594610.906191.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1eu8

1eu8


Resolution: 2.15→39.087 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.65
RfactorNum. reflection% reflection
Rfree0.2048 4624 4.95 %
Rwork0.1738 --
obs0.1754 93498 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.09 Å2 / Biso mean: 31.831 Å2 / Biso min: 13.88 Å2
Refinement stepCycle: final / Resolution: 2.15→39.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12424 0 96 514 13034
Biso mean--19.96 33.65 -
Num. residues----1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212950
X-RAY DIFFRACTIONf_angle_d0.6117613
X-RAY DIFFRACTIONf_chiral_restr0.0421943
X-RAY DIFFRACTIONf_plane_restr0.0052252
X-RAY DIFFRACTIONf_dihedral_angle_d15.5557722
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7100X-RAY DIFFRACTION6.322TORSIONAL
12B7100X-RAY DIFFRACTION6.322TORSIONAL
13C7100X-RAY DIFFRACTION6.322TORSIONAL
14D7100X-RAY DIFFRACTION6.322TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1481-2.17260.33171190.27972414253378
2.1726-2.19810.27721430.27032847299093
2.1981-2.22490.28321460.26022927307394
2.2249-2.25310.26411590.25512948310796
2.2531-2.28270.28021520.24572878303095
2.2827-2.3140.26411540.24012971312596
2.314-2.3470.27981570.23142945310295
2.347-2.38210.28961480.22952973312196
2.3821-2.41930.26711760.21962934311095
2.4193-2.45890.24991530.21332955310897
2.4589-2.50130.2271550.20762965312096
2.5013-2.54680.2571610.21612961312297
2.5468-2.59580.24771500.20672987313797
2.5958-2.64880.27861640.19883012317697
2.6488-2.70630.20631650.20042983314897
2.7063-2.76930.22281530.2033014316797
2.7693-2.83850.23261700.19872983315396
2.8385-2.91520.25591480.19533019316798
2.9152-3.0010.22011550.19443018317398
3.001-3.09780.23331430.18813060320397
3.0978-3.20850.20151440.1823014315897
3.2085-3.33690.2261460.17273047319397
3.3369-3.48870.19941590.16693021318097
3.4887-3.67250.18911700.15232993316397
3.6725-3.90240.16931500.14223045319596
3.9024-4.20330.15251520.12762999315196
4.2033-4.62570.1481500.1183015316595
4.6257-5.29370.14831670.12382981314894
5.2937-6.66410.17451570.14862984314193
6.6641-39.0930.1331580.12552981313989

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