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- PDB-7c6l: Crystal structure of beta-glycosides-binding protein (W177X) of A... -

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Basic information

Entry
Database: PDB / ID: 7c6l
TitleCrystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to cellotriose (Form II)
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 / CARBON DIOXIDE / DI(HYDROXYETHYL)ETHER / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 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
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,19812
Polymers91,8122
Non-polymers1,38610
Water5,891327
1
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6027
Polymers45,9061
Non-polymers6966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-21 kcal/mol
Surface area16580 Å2
MethodPISA
2
B: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5965
Polymers45,9061
Non-polymers6904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint3 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 100.340, 133.230
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: ARG / End label comp-ID: ARG / 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: 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 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80
#2: Polysaccharide alpha-L-altropyranose-(1-4)-alpha-D-altropyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LAltpa1-4DAltpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1222h-1a_1-5][a2111h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Altp]{[(4+1)][a-L-Altp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 335 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.22 Å3/Da / Density % sol: 44.72 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 60% 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 12, 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: 2.4→66.61 Å / Num. obs: 32723 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Rrim(I) all: 0.142 / Net I/σ(I): 11.4 / Num. measured all: 217551 / Scaling rejects: 106
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.490.5172068633370.9050.2190.5633.699.5
8.98-66.610.05445127260.9960.0230.05922.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.19 Å66.61 Å
Translation5.19 Å66.61 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: 2.4→66.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.823 / SU ML: 0.163 / SU R Cruickshank DPI: 0.6112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 1645 5 %RANDOM
Rwork0.1911 ---
obs0.1947 31019 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.87 Å2 / Biso mean: 28.456 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1--14.98 Å2-0 Å2-0 Å2
2--5.72 Å20 Å2
3---9.26 Å2
Refinement stepCycle: final / Resolution: 2.4→66.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 87 327 6774
Biso mean--28.55 26.79 -
Num. residues----831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176118
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6489017
X-RAY DIFFRACTIONr_angle_other_deg1.4141.56614178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0675829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10221.651315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.813151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3821542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021439
Refine LS restraints NCS

Ens-ID: 1 / Number: 12928 / 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: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 121 -
Rwork0.217 2228 -
all-2349 -
obs--99.24 %
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)
10.55140.41140.08630.8937-0.14840.44370.0241-0.02140.0216-0.0369-0.01240.01970.0716-0.0365-0.01170.03780.00250.00850.0415-0.02150.023-3.381622.61217.4916
21.58870.3070.19290.4363-0.03120.2807-0.0537-0.01670.1771-0.01560.00230.081-0.0472-0.06820.05140.01270.0183-0.00540.0332-0.00340.0601-18.078619.067150.5844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 416
2X-RAY DIFFRACTION2B2 - 417

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