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- PDB-8qlv: Crystal structure of the pneumococcal Substrate-binding protein A... -

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Basic information

Entry
Database: PDB / ID: 8qlv
TitleCrystal structure of the pneumococcal Substrate-binding protein AliB in complex with Peptide 4
Components
  • Oligopeptide-binding protein AliB
  • VAL-MET-VAL-LYS-GLY-PRO-GLY-PRO-GLY-ARG
KeywordsPEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AliB / peptide / substrate-binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Oligopeptide-binding protein AliB
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsAlcorlo, M. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-115331GB-I00 Spain
CitationJournal: Plos Pathog. / Year: 2024
Title: Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci.
Authors: Alcorlo, M. / Abdullah, M.R. / Steil, L. / Sotomayor, F. / Lopez-de Oro, L. / de Castro, S. / Velazquez, S. / Kohler, T.P. / Jimenez, E. / Medina, A. / Uson, I. / Keller, L.E. / Bradshaw, J. ...Authors: Alcorlo, M. / Abdullah, M.R. / Steil, L. / Sotomayor, F. / Lopez-de Oro, L. / de Castro, S. / Velazquez, S. / Kohler, T.P. / Jimenez, E. / Medina, A. / Uson, I. / Keller, L.E. / Bradshaw, J.L. / McDaniel, L.S. / Camarasa, M.J. / Volker, U. / Hammerschmidt, S. / Hermoso, J.A.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: VAL-MET-VAL-LYS-GLY-PRO-GLY-PRO-GLY-ARG
A: Oligopeptide-binding protein AliB


Theoretical massNumber of molelcules
Total (without water)71,0162
Polymers71,0162
Non-polymers00
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.759, 114.135, 58.977
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide VAL-MET-VAL-LYS-GLY-PRO-GLY-PRO-GLY-ARG


Mass: 999.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Oligopeptide-binding protein AliB


Mass: 70016.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: aliB, spr1382 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A4G1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium Acetate, 8% 2-Propanol and 21% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.49→47.41 Å / Num. obs: 99634 / % possible obs: 97.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.671 / Num. unique obs: 4851 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→47.41 Å / SU ML: 0.1705 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1749 4960 4.98 %
Rwork0.1381 94634 -
obs0.14 99594 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.42 Å2
Refinement stepCycle: LAST / Resolution: 1.49→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 0 802 5785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475125
X-RAY DIFFRACTIONf_angle_d0.71716947
X-RAY DIFFRACTIONf_chiral_restr0.0709747
X-RAY DIFFRACTIONf_plane_restr0.0052905
X-RAY DIFFRACTIONf_dihedral_angle_d16.60691895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.30131680.28073107X-RAY DIFFRACTION95.34
1.51-1.520.28131580.24593058X-RAY DIFFRACTION96.29
1.52-1.540.27721720.22443111X-RAY DIFFRACTION96.13
1.54-1.560.25681590.19253096X-RAY DIFFRACTION96.44
1.56-1.580.25221790.17493062X-RAY DIFFRACTION96.23
1.58-1.610.21561640.15363147X-RAY DIFFRACTION95.97
1.61-1.630.21161730.15223086X-RAY DIFFRACTION97.28
1.63-1.650.19681570.14713110X-RAY DIFFRACTION96.12
1.65-1.680.20441620.14473145X-RAY DIFFRACTION97.52
1.68-1.710.17571720.14463096X-RAY DIFFRACTION96.34
1.71-1.740.19851720.14743149X-RAY DIFFRACTION97.5
1.74-1.770.18641520.15193102X-RAY DIFFRACTION96.62
1.77-1.80.20441730.14563185X-RAY DIFFRACTION97.9
1.8-1.840.18611830.13353089X-RAY DIFFRACTION96.66
1.84-1.880.16571470.13453165X-RAY DIFFRACTION98.42
1.88-1.920.19111700.12573144X-RAY DIFFRACTION96.7
1.92-1.970.1841650.12263167X-RAY DIFFRACTION98.41
1.97-2.020.16191340.11873192X-RAY DIFFRACTION97.85
2.02-2.080.17321580.1223157X-RAY DIFFRACTION97.13
2.08-2.150.16361560.12013178X-RAY DIFFRACTION98.64
2.15-2.230.15561540.12293202X-RAY DIFFRACTION98.73
2.23-2.310.16311630.12883182X-RAY DIFFRACTION98.3
2.31-2.420.18781600.12713177X-RAY DIFFRACTION98.41
2.42-2.550.17461710.13863179X-RAY DIFFRACTION98.7
2.55-2.710.18831670.13963221X-RAY DIFFRACTION98.98
2.71-2.920.15741620.13893229X-RAY DIFFRACTION98.86
2.92-3.210.16881710.13573199X-RAY DIFFRACTION99.15
3.21-3.670.15691860.12913206X-RAY DIFFRACTION99.21
3.67-4.630.1491830.12343217X-RAY DIFFRACTION99.3
4.63-47.410.16161690.15543276X-RAY DIFFRACTION99.34

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