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- PDB-7c70: Crystal structure of beta-glycosides-binding protein (W67A) of AB... -

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Basic information

Entry
Database: PDB / ID: 7c70
TitleCrystal structure of beta-glycosides-binding protein (W67A) 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 / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / PHOSPHATE ION / SULFUR DIOXIDE / SULFITE ION / Sugar ABC transporter, periplasmic sugar-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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 / 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

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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)93,83022
Polymers91,8162
Non-polymers2,01420
Water14,988832
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,80710
Polymers45,9081
Non-polymers8999
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02312
Polymers45,9081
Non-polymers1,11511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.240, 98.960, 66.560
Angle α, β, γ (deg.)90.000, 103.250, 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: 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

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 45908.156 Da / Num. of mol.: 2 / Mutation: W67A
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-(1-6)-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 , 10 types, 850 molecules

#3: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2S
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 1.93 Å3/Da / Density % sol: 36.36 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 55% 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 11, 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: 1.63→49.53 Å / Num. obs: 85916 / % possible obs: 99 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/σ(I): 15.9
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
1.63-1.666.70.4232790441420.9180.1740.458497
8.92-49.487.20.06440525630.9960.0250.06933.199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.91 Å49.48 Å
Translation4.91 Å49.48 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C63

7c63


Resolution: 1.63→49.48 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.126 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 4157 4.8 %RANDOM
Rwork0.14 ---
obs0.1418 81727 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.21 Å2 / Biso mean: 16.092 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-0.15 Å2
2--0.85 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.63→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 125 832 7304
Biso mean--34.82 26.04 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0136804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176331
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.6549277
X-RAY DIFFRACTIONr_angle_other_deg1.5941.57714699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98521.902326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.276151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7331543
X-RAY DIFFRACTIONr_chiral_restr0.1030.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021473
Refine LS restraints NCS

Ens-ID: 1 / Number: 13309 / 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: 1.63→1.671 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.236 313 -
Rwork0.202 5905 -
obs--96.91 %
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)
10.1549-0.10880.03120.1301-0.03690.09130.00060.0165-0.00840.0181-0.00590.0076-0.01020.00270.00530.00840.00250.00350.00250.00030.009814.6535-13.885117.8703
20.2281-0.01110.10340.09060.01260.05940.01620.01190.00320.0006-0.0033-0.00410.00830.0041-0.01280.00150.00270.00020.01620.00490.018521.2623-15.9068-12.4415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 416
2X-RAY DIFFRACTION2B2 - 416

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