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- PDB-7c63: Crystal structure of beta-glycosides-binding protein of ABC trans... -

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Basic information

Entry
Database: PDB / ID: 7c63
TitleCrystal structure of beta-glycosides-binding protein of ABC transporter in an open state (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 / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / 2-HYDROXY BUTANE-1,4-DIOL / SULFITE ION / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsKanaujia, S.P. / Chandravanshi, M.
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 21, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,5908
Polymers46,0231
Non-polymers5677
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 62.930, 104.020
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 , 1 types, 1 molecules A

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


Mass: 46023.289 Da / Num. of mol.: 1
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: TTHB082 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80

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Non-polymers , 7 types, 471 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.16 % / Description: orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulphate, 30% 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: Nov 19, 2016 / 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→51 Å / Num. obs: 48845 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Rrim(I) all: 0.052 / Net I/σ(I): 24.7 / Num. measured all: 440139 / Scaling rejects: 24
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
1.63-1.668.20.3091965323970.9610.1150.334.999.8
8.92-517.80.02281836310.0080.02252.699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.84 Å51 Å
Translation6.84 Å51 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.83phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UOR

3uor


Resolution: 1.63→51 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.775 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2376 4.9 %RANDOM
Rwork0.164 ---
obs0.1661 46399 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.42 Å2 / Biso mean: 22.092 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å2-0 Å2-0 Å2
2--0.6 Å20 Å2
3---3.02 Å2
Refinement stepCycle: final / Resolution: 1.63→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 32 464 3681
Biso mean--38.01 32.24 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173108
X-RAY DIFFRACTIONr_angle_refined_deg2.1631.6434585
X-RAY DIFFRACTIONr_angle_other_deg1.6411.5747204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.1325.391448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20421.667162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29915507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4331522
X-RAY DIFFRACTIONr_chiral_restr0.120.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
LS refinement shellResolution: 1.63→1.671 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.257 178 -
Rwork0.17 3372 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -23.5336 Å / Origin y: -1.1065 Å / Origin z: 13.6286 Å
111213212223313233
T0.0147 Å2-0.0072 Å20.0054 Å2-0.009 Å20.0015 Å2--0.0116 Å2
L0.4657 °2-0.005 °20.0673 °2-0.4309 °20.0089 °2--0.3694 °2
S-0.0054 Å °-0.0171 Å °0.0148 Å °-0.0103 Å °-0.0225 Å °-0.0327 Å °-0.0347 Å °0.0205 Å °0.0279 Å °

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