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- PDB-7c6g: Crystal structure of beta-glycosides-binding protein (W177X) of A... -

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Basic information

Entry
Database: PDB / ID: 7c6g
TitleCrystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to gentiobiose
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
CARBON DIOXIDE / S-1,2-PROPANEDIOL / SULFITE ION / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 9, 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
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,15414
Polymers91,8122
Non-polymers1,34112
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-5 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 91.540, 69.390
Angle α, β, γ (deg.)90.000, 112.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 414 / Label seq-ID: 2 - 415

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

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 45906.211 Da / Num. of mol.: 2 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80
#2: Polysaccharide beta-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 480 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.38 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 45% 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: Feb 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: 1.9→48.75 Å / Num. obs: 53435 / % possible obs: 94.5 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Net I/σ(I): 10.6 / Num. measured all: 252521 / Scaling rejects: 459
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.940.4311497732580.8910.2190.4852.889.3
9.11-48.750.06524425350.9920.0350.07419.398.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.93 Å48.75 Å
Translation4.93 Å48.75 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: 1.9→48.75 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.825 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2572 4.8 %RANDOM
Rwork0.1735 ---
obs0.1761 50810 94.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.67 Å2 / Biso mean: 27.588 Å2 / Biso min: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.98 Å2-0 Å2-2.2 Å2
2--3.23 Å20 Å2
3---3.75 Å2
Refinement stepCycle: final / Resolution: 1.9→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 80 470 6946
Biso mean--39.44 32.03 -
Num. residues----835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176189
X-RAY DIFFRACTIONr_angle_refined_deg1.921.6539129
X-RAY DIFFRACTIONr_angle_other_deg1.4771.57714345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68721.579323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.448151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0941544
X-RAY DIFFRACTIONr_chiral_restr0.0950.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021463
Refine LS restraints NCS

Ens-ID: 1 / Number: 13229 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 190 -
Rwork0.188 3531 -
all-3721 -
obs--88.38 %
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)
10.82450.1385-0.01740.2014-0.13110.3685-0.0033-0.0842-0.01130.0111-0.00320.0045-0.0614-0.00770.00660.04310.0099-0.01380.02450.00090.006-3.7579-6.417228.3487
20.7768-0.15650.01820.2376-0.14320.45620.01210.0790.0769-0.007-0.0316-0.02240.02930.02090.01950.00310.0028-0.00130.05990.01970.02568.70178.576-0.4766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 419
2X-RAY DIFFRACTION2B1 - 415

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