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

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Basic information

Entry
Database: PDB / ID: 8qlm
TitleCrystal structure of the pneumococcal Substrate-binding protein AliB in complex with Peptide 3
Components
  • Oligopeptide-binding protein AliB
  • PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL
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 / 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: 1.66 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
A: Oligopeptide-binding protein AliB
B: Oligopeptide-binding protein AliB
C: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL
D: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)142,0194
Polymers142,0194
Non-polymers00
Water22,6631258
1
A: Oligopeptide-binding protein AliB
C: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)71,0102
Polymers71,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-10 kcal/mol
Surface area24360 Å2
2
B: Oligopeptide-binding protein AliB
D: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)71,0102
Polymers71,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area24410 Å2
Unit cell
Length a, b, c (Å)64.204, 108.837, 86.643
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oligopeptide-binding protein AliB


Mass: 70016.430 Da / Num. of mol.: 2
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
#2: Protein/peptide PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Mass: 993.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
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 PILATUS 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: 1.66→47.02 Å / Num. obs: 134554 / % possible obs: 97.6 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.9
Reflection shellResolution: 1.66→1.71 Å / Rmerge(I) obs: 0.792 / Num. unique obs: 6595 / CC1/2: 0.77

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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: 1.66→47.02 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 6737 5.01 %
Rwork0.1663 127738 -
obs0.1683 134475 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.11 Å2 / Biso mean: 29.3002 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.66→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9970 0 0 1258 11228
Biso mean---37.08 -
Num. residues----1264
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.66-1.67890.29732170.2573419896
1.6789-1.69860.31122420.2451417696
1.6986-1.71930.2742150.2341418096
1.7193-1.74110.26082180.2238418896
1.7411-1.7640.28072310.2148417796
1.764-1.78820.262530.214420596
1.7882-1.81370.26112360.2064416796
1.8137-1.84080.26952310.1969419497
1.8408-1.86960.24112400.1869416697
1.8696-1.90020.23062230.1808423697
1.9002-1.9330.27592310.1925423597
1.933-1.96810.2352390.1845422297
1.9681-2.0060.22262140.1685428397
2.006-2.04690.23822000.1707423297
2.0469-2.09150.22141920.1693423597
2.0915-2.14010.20472350.1648429397
2.1401-2.19360.18212120.1567420597
2.1936-2.25290.2242300.1648426398
2.2529-2.31920.22592240.1739427798
2.3192-2.39410.23641950.1687428798
2.3941-2.47960.20582210.1696432698
2.4796-2.57890.21282150.1729431398
2.5789-2.69630.19662150.1624427298
2.6963-2.83840.20622260.1648430598
2.8384-3.01620.20192180.1678432399
3.0162-3.24910.20852450.1593433499
3.2491-3.57590.17152120.1481434299
3.5759-4.09310.15312330.1404434799
4.0931-5.15590.16882070.1419438299
5.1559-47.020.19232670.1704437599
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)
11.6647-0.1215-0.15180.9396-0.35290.5603-0.08430.13920.07-0.10480.05410.03950.0168-0.07120.02220.1459-0.0117-0.02490.12850.00880.13676.079526.863929.5459
20.54560.4275-0.16790.7951-0.56740.6213-0.10810.0287-0.1998-0.0913-0.0789-0.34380.1460.1290.15430.17370.01260.03820.15480.03020.297130.123214.379433.4928
30.7491-0.25050.11481.7755-0.34880.5484-0.0164-0.0501-0.12350.0350.03140.03880.0684-0.0495-0.01490.14620.00240.00880.14030.01590.150110.4941.204449.1027
40.92610.2325-0.04750.9737-0.4980.5566-0.0916-0.08540.09070.166-0.039-0.1682-0.09130.03560.12760.16820.0119-0.04240.1321-0.00610.171221.283424.28445.8317
51.86680.05980.09620.80040.07360.7327-0.0624-0.03120.1835-0.1066-0.06920.1229-0.076-0.06550.11250.15130.012-0.02950.137-0.03530.137132.081628.43271.524
62.12270.81770.27081.45080.07630.31910.1166-0.5246-0.44110.1644-0.1631-0.1220.0746-0.02860.04320.2172-0.01210.00730.29050.09290.171540.03567.013885.9454
70.8480.24050.6830.08160.02072.8093-0.04550.5374-0.7297-0.6647-0.2826-0.83470.99791.10220.26890.50860.1450.19140.44460.00410.683318.47197.773337.5656
80.2246-0.2680.61090.7002-1.15872.1467-0.13220.5568-0.5239-0.6697-0.3762-0.80810.99250.86320.4160.63260.02020.32310.5062-0.05440.675942.29988.137577.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 220 )A29 - 220
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 303 )A221 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 553 )A304 - 553
4X-RAY DIFFRACTION4chain 'A' and (resid 554 through 649 )A554 - 649
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 242 )B29 - 242
6X-RAY DIFFRACTION6chain 'B' and (resid 243 through 649 )B243 - 649
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 11 )C1 - 11
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 11 )D1 - 11

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