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- PDB-7c69: Crystal structure of beta-glycosides-binding protein of ABC trans... -

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Basic information

Entry
Database: PDB / ID: 7c69
TitleCrystal structure of beta-glycosides-binding protein of ABC transporter in a closed state bound to sophorose
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 / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,99710
Polymers92,0472
Non-polymers9518
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-28 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.790, 108.930, 109.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 415 / Label seq-ID: 3 - 416

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 46023.289 Da / Num. of mol.: 2
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
#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 40.08 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulphate, 35% 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 19, 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: 2.35→62.79 Å / Num. obs: 32179 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.984 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.071 / Rrim(I) all: 0.214 / Net I/σ(I): 9.6 / Num. measured all: 279970 / Scaling rejects: 405
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
2.35-2.438.10.5082507831100.9010.1880.5433.899.7
9.1-62.797.60.13648456400.9830.0510.14514.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.08 Å54.99 Å
Translation5.08 Å54.99 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: 2.35→55.06 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.236 / SU ML: 0.212 / SU R Cruickshank DPI: 0.6542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.654 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1704 5.3 %RANDOM
Rwork0.1996 ---
obs0.203 30415 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.88 Å2 / Biso mean: 26.38 Å2 / Biso min: 1.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--1.32 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 2.35→55.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6387 0 58 264 6709
Biso mean--21.91 26.04 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176104
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.659017
X-RAY DIFFRACTIONr_angle_other_deg1.371.57714145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37622.07314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.703151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021436
Refine LS restraints NCS

Ens-ID: 1 / Number: 12832 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 139 -
Rwork0.215 2212 -
all-2351 -
obs--99.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71830.0146-0.0950.58830.16030.3172-0.01030.0043-0.03650.03290.02-0.0145-0.0119-0.0123-0.00970.11010.0057-0.00830.00310.00530.0295-4.4606-16.723328.3208
20.5433-0.1305-0.3740.38090.14140.78730.0099-0.0250.0408-0.0305-0.0260.01410.02840.02360.01610.0959-0.0105-0.00090.01920.00970.0201-19.1657-1.79196.5499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 416
2X-RAY DIFFRACTION2B2 - 419

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