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- PDB-6jad: Crystal structure of ABC transporter alpha-glycoside-binding prot... -

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Basic information

Entry
Database: PDB / ID: 6jad
TitleCrystal structure of ABC transporter alpha-glycoside-binding protein in complex with palatinose
ComponentsABC transporter, periplasmic substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-bindingsite / alpha-glycoside-binding protein / Ligand selection / Multi-substrate transporter / Sugar replacement / Venus Fly-trap mechanism
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ABC transporter, periplasmic substrate-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. / Gogoi, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/563/NE/U-Excel/2016 India
CitationJournal: Febs J. / Year: 2020
Title: Structural and thermodynamic correlation illuminates the selective transport mechanism of disaccharide alpha-glycosides through ABC transporter.
Authors: Chandravanshi, M. / Gogoi, P. / Kanaujia, S.P.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8954
Polymers46,1681
Non-polymers7273
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint3 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.770, 84.770, 145.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21A-971-

HOH

31A-1115-

HOH

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Components

#1: Protein ABC transporter, periplasmic substrate-binding protein / alpha-GlyBP


Mass: 46168.000 Da / Num. of mol.: 1
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: TTHA0356 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SLD7
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DFrufa2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2a_2-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.11 % / Description: Tetragonal
Crystal growTemperature: 277 K / Method: microbatch / pH: 5
Details: 0.05 M Citric Acid, 0.05 M Bis-Tris Propane, 16% PEG 3350

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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 27, 2018 / 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→73.29 Å / Num. obs: 42666 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.05 / Rrim(I) all: 0.097 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→9.11 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2695 / CC1/2: 0.915 / Rpim(I) all: 0.268 / Rrim(I) all: 0.524 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.46 Å59.94 Å
Translation6.46 Å59.94 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
iMOSFLM7.2.2data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
Coot0.8.9.1model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9W

6j9w


Resolution: 1.9→73.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.263 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2097 4.9 %RANDOM
Rwork0.1394 ---
obs0.1415 40512 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.84 Å2 / Biso mean: 22.409 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-0 Å2
2--0.84 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 1.9→73.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 49 517 3793
Biso mean--30.45 34.22 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193390
X-RAY DIFFRACTIONr_bond_other_d0.0010.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9574622
X-RAY DIFFRACTIONr_angle_other_deg0.90237099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73822.695167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36315533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4861535
X-RAY DIFFRACTIONr_chiral_restr0.1160.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 136 -
Rwork0.175 2925 -
all-3061 -
obs--99.48 %

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