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- PDB-7c6f: Crystal structure of beta-glycosides-binding protein (W177X) of A... -

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Basic information

Entry
Database: PDB / ID: 7c6f
TitleCrystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open state
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 / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / SULFITE ION / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 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 16, 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

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)46,54211
Polymers45,9061
Non-polymers63510
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.210, 63.100, 103.790
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: 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 (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 , 6 types, 411 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.08 Å3/Da / Density % sol: 40.87 % / 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: Apr 9, 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: 1.7→53.92 Å / Num. obs: 41913 / % possible obs: 98.1 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Net I/σ(I): 14.5 / Num. measured all: 278893 / Scaling rejects: 156
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
1.7-1.736.20.3721275820610.9220.1560.4054.294
9-53.925.70.09120143550.9910.0390.09922.799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6 Å53.92 Å
Translation6 Å53.92 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

7c63


Resolution: 1.7→53.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.141 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 2116 5.1 %RANDOM
Rwork0.1737 ---
obs0.1759 39744 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.71 Å2 / Biso mean: 23.409 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.7→53.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 34 401 3620
Biso mean--39.8 31.44 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133331
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173088
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.6434532
X-RAY DIFFRACTIONr_angle_other_deg1.5621.5697158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43921.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5915513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0951521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 161 -
Rwork0.219 2740 -
all-2901 -
obs--93.73 %
Refinement TLS params.Method: refined / Origin x: 23.2658 Å / Origin y: -1.2772 Å / Origin z: -13.488 Å
111213212223313233
T0.0054 Å20.0013 Å2-0.0051 Å2-0.0059 Å2-0.0043 Å2--0.0103 Å2
L0.3833 °20.0021 °20.027 °2-0.3595 °20.1329 °2--0.2337 °2
S-0.0306 Å °0.0123 Å °-0.0056 Å °-0.0142 Å °-0.014 Å °0.02 Å °-0.027 Å °-0.008 Å °0.0446 Å °

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