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- PDB-4uac: EUR_01830 with acarbose -

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Basic information

Entry
Database: PDB / ID: 4uac
TitleEUR_01830 with acarbose
ComponentsCarbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-)
KeywordsTRANSPORT PROTEIN / solute-binding protein / acarbose / ABC transporter
Function / homology
Function and homology information


Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / DI(HYDROXYETHYL)ETHER / Carbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-)
Similarity search - Component
Biological speciesEubacterium rectale DSM 17629 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKoropatkin, N.M. / Orlovsky, N.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH 2 P30 DK 034933 United States
CitationJournal: Mol.Microbiol. / Year: 2015
Title: Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale.
Authors: Cockburn, D.W. / Orlovsky, N.I. / Foley, M.H. / Kwiatkowski, K.J. / Bahr, C.M. / Maynard, M. / Demeler, B. / Koropatkin, N.M.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6216
Polymers42,6831
Non-polymers9385
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.805, 110.408, 38.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Carbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-)


Mass: 42682.926 Da / Num. of mol.: 1 / Fragment: unp residues 40-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria)
Gene: EUR_01830 / Plasmid: pETite / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: D6E1Y1
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% pentaerythritol propoxylate 5/4 PO/OH, 0.2M NaCl, and 0.1 M 2-(N-morpholino)ethanesulfonic acid pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 55194 / % possible obs: 96.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.238 / % possible all: 75.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.85 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 2807 5.09 %
Rwork0.144 --
obs0.146 55121 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 63 475 3428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013022
X-RAY DIFFRACTIONf_angle_d1.3874103
X-RAY DIFFRACTIONf_dihedral_angle_d12.9021059
X-RAY DIFFRACTIONf_chiral_restr0.281458
X-RAY DIFFRACTIONf_plane_restr0.007538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5996-1.62720.1723920.15811980X-RAY DIFFRACTION75
1.6272-1.65680.19631210.15632153X-RAY DIFFRACTION81
1.6568-1.68860.2081240.15962320X-RAY DIFFRACTION87
1.6886-1.72310.19821270.16382525X-RAY DIFFRACTION94
1.7231-1.76060.2261290.17462616X-RAY DIFFRACTION98
1.7606-1.80150.19321460.15752676X-RAY DIFFRACTION100
1.8015-1.84660.19931550.15592686X-RAY DIFFRACTION100
1.8466-1.89650.19291390.15292661X-RAY DIFFRACTION100
1.8965-1.95230.17931390.14722696X-RAY DIFFRACTION100
1.9523-2.01530.18691460.14732705X-RAY DIFFRACTION100
2.0153-2.08730.16281560.1462642X-RAY DIFFRACTION100
2.0873-2.17090.18011410.14322727X-RAY DIFFRACTION100
2.1709-2.26960.19291590.14022687X-RAY DIFFRACTION100
2.2696-2.38920.1851380.13332704X-RAY DIFFRACTION100
2.3892-2.53890.15911550.14052697X-RAY DIFFRACTION100
2.5389-2.73480.15141230.142746X-RAY DIFFRACTION100
2.7348-3.00980.19881540.14792712X-RAY DIFFRACTION100
3.0098-3.44490.20261470.14632745X-RAY DIFFRACTION99
3.4449-4.33850.15751670.13352760X-RAY DIFFRACTION99
4.3385-31.860.14631490.13862876X-RAY DIFFRACTION98

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