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- PDB-7c6t: Crystal structure of beta-glycosides-binding protein (W177X) of A... -

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Basic information

Entry
Database: PDB / ID: 7c6t
TitleCrystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (Form I)
ComponentsSugar ABC transporter, periplasmic sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Conformational dynamics / substrate-binding protein / Induced-fit mechanism / Two-step ligand binding / Venus Fly-trap mechanism
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / CARBON DIOXIDE / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKanaujia, S.P. / Chandravanshi, M. / Samanta, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/563/NE/U-Excel/2016 India
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Conformational Trapping of a beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers.
Authors: Chandravanshi, M. / Samanta, R. / Kanaujia, S.P.
History
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,7548
Polymers45,9061
Non-polymers8487
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.930, 63.550, 110.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 45906.211 Da / Num. of mol.: 1 / Mutation: K174R, N175T, S176P, W177del, D178R, V179T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHB082 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.46 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 40% PEG 8000

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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: Sep 18, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→57.93 Å / Num. obs: 18713 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.037 / Rrim(I) all: 0.112 / Net I/σ(I): 16.1 / Num. measured all: 165548 / Scaling rejects: 684
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.388.50.3561503617710.9610.1230.3775.699.3
8.91-57.937.60.04729673880.9980.0170.0528.999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.1 Å55.06 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C63
Resolution: 2.3→55.06 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.674 / SU ML: 0.151 / SU R Cruickshank DPI: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 867 4.7 %RANDOM
Rwork0.2026 ---
obs0.2054 17774 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.22 Å2 / Biso mean: 24.888 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-6.23 Å20 Å20 Å2
2--7.72 Å20 Å2
3----13.95 Å2
Refinement stepCycle: final / Resolution: 2.3→55.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 54 139 3349
Biso mean--30.66 27.5 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173045
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.664494
X-RAY DIFFRACTIONr_angle_other_deg1.461.587057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6321.72157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8121521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 51 -
Rwork0.242 1288 -
all-1339 -
obs--98.82 %
Refinement TLS params.Method: refined / Origin x: 21.0734 Å / Origin y: 1.0922 Å / Origin z: 16.1819 Å
111213212223313233
T0.0138 Å2-0.0052 Å2-0.0139 Å2-0.0233 Å2-0.0017 Å2--0.0163 Å2
L0.7346 °2-0.1522 °2-0.2024 °2-0.7182 °20.2364 °2--0.8618 °2
S0.0311 Å °-0.0096 Å °-0.0428 Å °-0.0354 Å °-0.0813 Å °0.0661 Å °-0.0141 Å °-0.0957 Å °0.0501 Å °

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