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

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Basic information

Entry
Database: PDB / ID: 6jbe
TitleCrystal structure of ABC transporter alpha-glycoside-binding mutant protein W287A in complex with glucose
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
CITRIC ACID / CARBON DIOXIDE / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / ABC transporter, periplasmic substrate-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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

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Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8228
Polymers46,0531
Non-polymers7697
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-1 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.990, 84.990, 145.830
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-664-

HOH

21A-1005-

HOH

31A-1171-

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: 46052.867 Da / Num. of mol.: 1 / Mutation: W287A
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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 579 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 57.44 % / 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: Apr 23, 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: 1.75→73.43 Å / Num. obs: 52985 / % possible obs: 97 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Net I/σ(I): 17.4
Reflection shellResolution: 1.75→9.09 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2590 / CC1/2: 0.918 / Rpim(I) all: 0.238 / Rrim(I) all: 0.652 / % possible all: 88.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.46 Å55.56 Å
Translation6.46 Å55.56 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: 1.75→73.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.71 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 2574 4.9 %RANDOM
Rwork0.1389 ---
obs0.1407 50331 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.36 Å2 / Biso mean: 19.767 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.75→73.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 51 573 3842
Biso mean--34.97 32.33 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193382
X-RAY DIFFRACTIONr_bond_other_d0.0010.023086
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9544598
X-RAY DIFFRACTIONr_angle_other_deg0.91237128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82422.754167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15215533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4631535
X-RAY DIFFRACTIONr_chiral_restr0.110.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 177 -
Rwork0.212 3331 -
all-3508 -
obs--88.23 %

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