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

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Basic information

Entry
Database: PDB / ID: 8qlc
TitleCrystal structure of the pneumococcal Substrate-binding protein AliD in open conformation
ComponentsAliD
KeywordsPEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AliD / peptide / substrate-binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / protein transport / metal ion binding / plasma membrane
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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 / SAD / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: AliD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2622
Polymers70,2371
Non-polymers241
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area26610 Å2
Unit cell
Length a, b, c (Å)57.241, 93.003, 111.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AliD


Mass: 70237.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: aliD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2BJN6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 23% PEG3350 and 0.1 M Tris-HCl pH=8.0.

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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: Sep 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→48.75 Å / Num. obs: 64025 / % possible obs: 99.99 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 1.089 / Num. unique obs: 3371 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.748 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 2756 4.93 %
Rwork0.176 53139 -
obs0.1777 55895 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.56 Å2 / Biso mean: 32.369 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: final / Resolution: 1.8→48.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4942 0 1 548 5491
Biso mean--21.82 37.3 -
Num. residues----624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.83110.28361360.22072612
1.8311-1.86440.24731390.21352608
1.8644-1.90020.30671320.22672640
1.9002-1.9390.25651530.21992586
1.939-1.98120.25081310.20232632
1.9812-2.02720.25561500.19312644
2.0272-2.07790.24951480.19632594
2.0779-2.13410.2181560.18542621
2.1341-2.19690.21651270.17882643
2.1969-2.26780.22371220.18562657
2.2678-2.34890.24491370.18532619
2.3489-2.44290.21151170.17892666
2.4429-2.55410.21211290.18542664
2.5541-2.68880.21681300.18772665
2.6888-2.85720.23451170.19222688
2.8572-3.07780.26481500.1892648
3.0778-3.38740.20931490.182687
3.3874-3.87740.16911440.15932692
3.8774-4.88440.16891370.14332728
4.8844-48.7480.18561520.15972845
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)
12.9062-0.14410.73752.0318-0.83041.78970.1135-0.2018-0.17960.228-0.1094-0.05460.03360.0723-0.01090.1534-0.02530.00350.1336-0.01880.10422.09634.31743.783
20.6173-0.3919-0.60270.43620.25980.04980.12820.26890.2054-0.2306-0.05760.0632-0.0814-0.1511-0.07290.3060.0431-0.01380.30980.03030.299-0.5146.76316.239
31.20280.16730.32281.07660.9342.65630.0080.0380.0936-0.0567-0.00960.011-0.075-0.0627-0.00630.12070.01410.00750.13880.03680.140824.74530.4817.072
40.9644-0.5149-0.78831.3834-0.25520.51080.0976-0.08310.38840.1213-0.1146-0.3122-0.2360.26180.00220.2197-0.0596-0.04540.20950.03230.340310.17450.94931.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:243 )A29 - 243
2X-RAY DIFFRACTION2( CHAIN A AND RESID 244:304 )A244 - 304
3X-RAY DIFFRACTION3( CHAIN A AND RESID 305:573 )A305 - 573
4X-RAY DIFFRACTION4( CHAIN A AND RESID 574:652 )A574 - 652

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