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- PDB-6jam: Crystal structure of ABC transporter alpha-glycoside-binding muta... -

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Basic information

Entry
Database: PDB / ID: 6jam
TitleCrystal structure of ABC transporter alpha-glycoside-binding mutant protein R356A in complex with trehalose
ComponentsABC transporter, periplasmic substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-bindingsite / alpha-glycoside-binding protein / Ligand selection / Multi-substrate transporter / Sugar replacement / Venus Fly-trap mechanism
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / 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
trehalose / ACETATE ION / CITRIC ACID / DI(HYDROXYETHYL)ETHER / ABC transporter, periplasmic substrate-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsKanaujia, S.P. / Chandravanshi, M. / Gogoi, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/563/NE/U-Excel/2016 India
CitationJournal: Febs J. / Year: 2020
Title: Structural and thermodynamic correlation illuminates the selective transport mechanism of disaccharide alpha-glycosides through ABC transporter.
Authors: Chandravanshi, M. / Gogoi, P. / Kanaujia, S.P.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _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 2.1Nov 22, 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: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0128
Polymers46,0821
Non-polymers9307
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-2 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.070, 85.070, 146.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

21A-1022-

HOH

31A-1185-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ABC transporter, periplasmic substrate-binding protein / alpha-GlyBP


Mass: 46081.883 Da / Num. of mol.: 1 / Mutation: R356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0356 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q5SLD7
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 593 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.89 Å3/Da / Density % sol: 57.45 % / Description: Tetragonal
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.4
Details: 0.04 M Citric Acid, 0.06 M Bis-Tris Propane, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 4, 2018 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→73.55 Å / Num. obs: 67875 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Net I/σ(I): 22.1
Reflection shellResolution: 1.63→8.92 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3277 / CC1/2: 0.953 / Rpim(I) all: 0.194 / Rrim(I) all: 0.567 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.47 Å46.47 Å
Translation6.47 Å46.47 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
iMOSFLM7.2.2data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
Coot0.8.9.1model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9W

6j9w


Resolution: 1.63→73.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.138 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1659 3294 4.9 %RANDOM
Rwork0.1381 ---
obs0.1395 64378 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.98 Å2 / Biso mean: 19.422 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.63→73.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 62 587 3885
Biso mean--32.09 32.87 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193431
X-RAY DIFFRACTIONr_bond_other_d0.0010.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9554669
X-RAY DIFFRACTIONr_angle_other_deg0.92637225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98322.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41115539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6971536
X-RAY DIFFRACTIONr_chiral_restr0.120.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
LS refinement shellResolution: 1.629→1.671 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 255 -
Rwork0.175 4672 -
all-4927 -
obs--100 %

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