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- PDB-8ula: Lmo2839 ABC transporter substrate binding protein -

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Basic information

Entry
Database: PDB / ID: 8ula
TitleLmo2839 ABC transporter substrate binding protein
ComponentsExtracellular solute-binding protein
KeywordsSUGAR BINDING PROTEIN / ABC transporter / substrate binding / extracellular
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Extracellular solute-binding protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRipley, B.M. / Radoshevich, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007343 United States
CitationJournal: To Be Published
Title: Structure of Listeria ABC transport substrate binding protein
Authors: Ripley, B.M. / Radoshevich, L.
History
DepositionOct 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)46,8111
Polymers46,8111
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.881, 95.881, 78.702
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Extracellular solute-binding protein / Sugar ABC transporter substrate-binding protein


Mass: 46811.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_11545, ARL18_04440, B5G90_11060, D4V33_03830, D5299_03735, D5W00_06110, DG57_01345, DOV25_04275, GCV64_11235, GT011_11725, GYO01_09805, GYU24_11900
Variant: EGDe / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A468ZWJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 3.5M NH4SO4, 0.1M MES sodium salt pH 6.5, and 1% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→57.12 Å / Num. obs: 58116 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.84 Å2 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.235 / Net I/σ(I): 2.5
Reflection shellResolution: 2→2.08 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2649 / Rpim(I) all: 0.39 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→57.12 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2291 1382 4.89 %
Rwork0.1876 26874 -
obs0.1894 28256 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.97 Å2
Refinement stepCycle: LAST / Resolution: 2→57.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 0 202 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253133
X-RAY DIFFRACTIONf_angle_d0.52334235
X-RAY DIFFRACTIONf_chiral_restr0.0411474
X-RAY DIFFRACTIONf_plane_restr0.003553
X-RAY DIFFRACTIONf_dihedral_angle_d15.02721175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.28291570.23932649X-RAY DIFFRACTION99.89
2.08-2.160.25161520.21622634X-RAY DIFFRACTION99.79
2.16-2.260.24611240.20082674X-RAY DIFFRACTION99.75
2.26-2.380.24681290.17692684X-RAY DIFFRACTION99.68
2.38-2.520.21631550.19542642X-RAY DIFFRACTION98.66
2.52-2.720.25881640.19322632X-RAY DIFFRACTION99.82
2.72-2.990.24511310.20392704X-RAY DIFFRACTION99.82
2.99-3.430.24531480.18432710X-RAY DIFFRACTION99.65
3.43-4.310.19341200.16362707X-RAY DIFFRACTION98.26
4.32-57.120.20911020.18982838X-RAY DIFFRACTION98.29

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