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

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Basic information

Entry
Database: PDB / ID: 8qlh
TitleCrystal structure of the pneumococcal Substrate-binding protein AliC as a domain-swapped dimer
ComponentsAliC
KeywordsPEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AliC / peptide / substrate-binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 19, 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

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Assembly

Deposited unit
A: AliC


Theoretical massNumber of molelcules
Total (without water)70,4601
Polymers70,4601
Non-polymers00
Water2,324129
1
A: AliC

A: AliC


Theoretical massNumber of molelcules
Total (without water)140,9202
Polymers140,9202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10280 Å2
ΔGint-53 kcal/mol
Surface area51020 Å2
Unit cell
Length a, b, c (Å)186.215, 60.514, 63.697
Angle α, β, γ (deg.)90.000, 96.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AliC


Mass: 70460.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: aliC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2BJN5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH=6.5 and 25% PEG3350

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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: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.38→57.52 Å / Num. obs: 28215 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 0.99 / Net I/σ(I): 11.2
Reflection shellResolution: 2.38→2.46 Å / Rmerge(I) obs: 0.657 / Num. unique obs: 2820 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→57.519 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1472 5.22 %
Rwork0.176 26729 -
obs0.1787 28201 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.2 Å2 / Biso mean: 58.4017 Å2 / Biso min: 29.08 Å2
Refinement stepCycle: final / Resolution: 2.38→57.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 0 129 5043
Biso mean---52.14 -
Num. residues----625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.38-2.45690.34881250.2881243099
2.4569-2.54470.33351360.2603240699
2.5447-2.64660.33011510.242238898
2.6466-2.7670.31641160.2321242899
2.767-2.91290.24321410.2148242999
2.9129-3.09540.32781240.2214239599
3.0954-3.33430.24571170.2008244798
3.3343-3.66980.2211490.1779237798
3.6698-4.20070.2061420.14842473100
4.2007-5.29190.18361480.1379242198
5.2919-57.5190.17471230.1417253599
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)
11.11210.4306-0.80311.8751-0.57182.61320.0741-0.04360.16770.1793-0.06490.1803-0.1066-0.2502-0.02120.5589-0.0081-0.00930.357-0.02130.408166.161827.380429.9762
21.2789-0.4879-0.75410.22910.40510.71980.2970.12670.3457-0.2078-0.08330.0195-0.03-0.1288-0.09050.71470.00310.03730.34690.02620.442194.307321.8497-3.2717
31.2382-0.2756-0.67061.39950.07453.0979-0.0063-0.2118-0.04960.06940.0395-0.1160.26780.58690.01170.47170.0827-0.01310.403-0.01520.3467122.9605-0.1867-5.0401
40.8458-0.3455-0.40461.1257-0.27731.85690.04870.15560.0324-0.0675-0.00350.10450.0434-0.1941-0.1310.53340.03010.01590.3243-0.02220.3604105.143316.9424-19.7217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 266 )A31 - 266
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 307 )A267 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 576 )A308 - 576
4X-RAY DIFFRACTION4chain 'A' and (resid 577 through 655 )A577 - 655

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