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

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Basic information

Entry
Database: PDB / ID: 8qlg
TitleCrystal structure of the pneumococcal Substrate-binding protein AliD in closed conformation in complex with Peptide 1
Components
  • AliD
  • Peptide 1
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)
Prevotella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
E: Peptide 1
B: AliD
C: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,13024
Polymers141,8224
Non-polymers1,30820
Water10,773598
1
A: AliD
E: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,69614
Polymers70,9112
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-192 kcal/mol
Surface area24970 Å2
2
B: AliD
C: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,43410
Polymers70,9112
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-235 kcal/mol
Surface area25080 Å2
Unit cell
Length a, b, c (Å)52.038, 67.089, 109.448
Angle α, β, γ (deg.)84.050, 87.260, 71.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AliD


Mass: 70237.375 Da / Num. of mol.: 2
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: Protein/peptide Peptide 1


Mass: 673.756 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Prevotella (bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 150 mM Zn Acetate, 10% PEG8000, 0.1 M MES pH=6.5

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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: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→46.63 Å / Num. obs: 94495 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.82 / Num. unique obs: 4650 / CC1/2: 0.78

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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: 2.1→45.266 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 3934 4.96 %
Rwork0.1909 75338 -
obs0.1928 79272 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124 Å2 / Biso mean: 41.3174 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: final / Resolution: 2.1→45.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 20 598 10598
Biso mean--60.79 42.09 -
Num. residues----1260
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12560.32341390.2725260096
2.1256-2.15250.33571250.2653271896
2.1525-2.18080.26691430.2498265096
2.1808-2.21070.29551430.2457264196
2.2107-2.24230.33021480.2445271596
2.2423-2.27580.27771450.2274267897
2.2758-2.31130.251480.2224267997
2.3113-2.34920.30641390.2215266197
2.3492-2.38970.26191350.2237268897
2.3897-2.43320.29631200.2195272497
2.4332-2.480.28161590.2144272598
2.48-2.53060.24331310.2059265197
2.5306-2.58560.26721530.1977273097
2.5856-2.64570.24221530.2048263697
2.6457-2.71190.21921320.1945272498
2.7119-2.78520.27151310.1958270297
2.7852-2.86720.23371460.1991269198
2.8672-2.95970.25311340.2039270698
2.9597-3.06540.26871210.2057274297
3.0654-3.18820.22461510.1954268998
3.1882-3.33320.21661260.1861269697
3.3332-3.50890.23971560.1816270498
3.5089-3.72860.17621440.1635275398
3.7286-4.01640.21321260.1569267298
4.0164-4.42020.17861600.1538267497
4.4202-5.05910.18731450.1494268097
5.0591-6.37110.20331490.1861272198
6.3711-45.2660.16971320.1925268897
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)
11.15430.26-0.14461.5130.6041.2807-0.02080.02410.0879-0.22520.060.0168-0.14130.0355-0.01950.1907-0.020.02340.14690.01860.1531-1.582327.7784-68.3131
20.29160.0570.31660.62830.22450.33610.0114-0.4334-0.20630.3089-0.02060.08940.3365-0.23630.05480.4376-0.08310.07980.45080.04530.337-14.15958.794-47.0415
31.7342-0.0753-0.47460.58570.39271.4533-0.0778-0.65020.21290.08340.02640.0250.03580.03150.0260.21260.0288-0.00740.4801-0.11390.235-5.580432.9148-36.0575
40.9471-0.03640.01130.9960.52711.1995-0.0678-0.2289-0.15360.25470.0812-0.18460.30510.1393-0.00730.26470.0125-0.01280.23780.04250.23843.342511.6448-53.9232
58.66364.77563.02973.22080.9096.7121-0.1997-0.50790.01870.7452-0.35280.79120.6196-0.8860.19990.2679-0.01720.10420.2787-0.04320.309-9.102525.7211-51.0563
61.5638-0.16030.03421.44041.00371.90480.04480.0366-0.1790.2279-0.01490.02290.21880.0381-0.00920.2083-0.0123-0.02230.1190.02320.16033.4793-2.282819.1464
70.5563-0.32880.00841.1106-1.10251.27980.01660.79380.1985-0.6535-0.1710.3712-0.3395-0.5352-0.02060.67320.1183-0.14140.58120.05940.3956-12.164821.109-0.3488
80.7681-0.39990.09470.533-0.33381.09380.12560.8719-0.2322-0.0956-0.32170.1036-0.1244-0.33-0.25250.25650.1661-0.0120.7303-0.33350.3114-6.9448-7.6191-14.7166
91.6191-0.099-0.00640.68790.4531.19280.12630.6809-0.208-0.1357-0.17910.0688-0.0448-0.11230.00320.24130.0777-0.02750.549-0.15960.27391.2879-5.8257-12.3201
101.0375-0.22810.15251.10560.71530.96740.04040.37080.1716-0.3308-0.0311-0.2557-0.4210.2123-0.020.3337-0.01820.0630.31120.07050.27458.807813.85534.9969
116.776-1.2124-1.60212.26111.47945.1661-0.04110.64930.1223-0.4642-0.05320.4481-0.4184-0.71860.02330.28930.1222-0.0250.5675-0.04940.2902-3.97820.24631.7367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 243 )A29 - 243
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 304 )A244 - 304
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 573 )A305 - 573
4X-RAY DIFFRACTION4chain 'A' and (resid 574 through 652 )A574 - 652
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 6 )E1 - 6
6X-RAY DIFFRACTION6chain 'B' and (resid 29 through 243 )B29 - 243
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 289 )B244 - 289
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 341 )B290 - 341
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 573 )B342 - 573
10X-RAY DIFFRACTION10chain 'B' and (resid 574 through 652 )B574 - 652
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 6 )C1 - 6

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