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

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Basic information

Entry
Database: PDB / ID: 8qlk
TitleCrystal structure of the pneumococcal Substrate-binding protein AliB in complex with Peptide 2
Components
  • ALA-ILE-GLN-SER-GLU-LYS-ALA-ARG-LYS-HIS-ASN
  • Oligopeptide-binding protein AliB
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: 2.29 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: ALA-ILE-GLN-SER-GLU-LYS-ALA-ARG-LYS-HIS-ASN


Theoretical massNumber of molelcules
Total (without water)71,3022
Polymers71,3022
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-1 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.976, 111.501, 56.280
Angle α, β, γ (deg.)90.00, 108.04, 90.00
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.: 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
#2: Protein/peptide ALA-ILE-GLN-SER-GLU-LYS-ALA-ARG-LYS-HIS-ASN


Mass: 1285.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
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: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.29→48.244 Å / Num. obs: 27597 / % possible obs: 98.6 % / Redundancy: 4.5 % / CC1/2: 0.995 / Net I/σ(I): 10.7
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.695 / Num. unique obs: 1767 / CC1/2: 0.85 / Rpim(I) all: 0.359

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.244 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 1374 4.98 %
Rwork0.1654 --
obs0.1681 27565 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→48.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 0 235 5240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035148
X-RAY DIFFRACTIONf_angle_d0.626978
X-RAY DIFFRACTIONf_dihedral_angle_d3.7544262
X-RAY DIFFRACTIONf_chiral_restr0.043753
X-RAY DIFFRACTIONf_plane_restr0.004908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.37190.28571440.20742608X-RAY DIFFRACTION98
2.3719-2.46690.30141120.20872617X-RAY DIFFRACTION98
2.4669-2.57910.27431460.20852575X-RAY DIFFRACTION98
2.5791-2.71510.27751500.19512562X-RAY DIFFRACTION97
2.7151-2.88520.2721580.17682587X-RAY DIFFRACTION98
2.8852-3.10790.25321210.17972661X-RAY DIFFRACTION99
3.1079-3.42060.21211350.1642612X-RAY DIFFRACTION99
3.4206-3.91540.18371360.14882632X-RAY DIFFRACTION99
3.9154-4.93220.18191430.13462661X-RAY DIFFRACTION99
4.9322-48.2440.17661290.15462676X-RAY DIFFRACTION99
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)
10.3447-0.09720.13080.50430.26450.3-0.00110.0678-0.039-0.04630.0267-0.06010.09530.0135-00.1447-0.0346-0.0050.14020.01040.170217.958-28.5874.45
20.3953-0.11760.12290.2850.23140.3787-0.00340.0156-0.00060.02020.0398-0.06540.04640.096400.1141-0.021-0.00690.13250.00290.123921.842-25.9578.091
30.41580.1936-0.06770.35150.4650.421-0.03760.09060.0526-0.1019-0.0032-0.0141-0.1163-0.0162-00.1991-0.0078-0.01420.1628-0.0060.18262.455-6.069-5.306
40.230.00890.18540.5213-0.06750.49820.0101-0.08460.00390.0346-0.05230.1014-0.0405-0.2218-0.00010.11440.00970.01230.1729-0.03570.1556-5.236-1.03616.962
50.2517-0.1002-0.1830.36030.40880.3142-0.006-0.0460.0737-0.05610.0375-0.067-0.0514-0.064-00.1644-0.0007-0.0130.14420.00520.17247.8111.0799.55
60.1732-0.09120.11540.07330.00390.08730.0361-0.4329-0.01750.2078-0.1073-0.18210.00740.0223-0.00060.3262-0.0018-0.02130.2448-0.01380.19810.335-9.14828.033
70.4956-0.00230.2260.24220.13020.48480.0398-0.0287-0.09130.0366-0.02940.05980.0416-0.112100.1476-0.0420.01530.19860.01010.1678-1.183-24.0635.247
80.0073-0.00420.00350.0057-0.00520.00710.04780.04810.2034-0.0666-0.13620.1836-0.1192-0.14470.00010.2698-0.04330.08290.24290.03770.2898.973-9.7525.685
90.0015-0.00180.01250.0048-0.00980.00020.0798-0.059-0.24540.0558-0.16050.2494-0.17420.0310.00050.55150.13130.00880.497-0.01520.3824.393-8.426-2.591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 32:125 )A32 - 125
2X-RAY DIFFRACTION2( CHAIN A AND RESID 126:242 )A126 - 242
3X-RAY DIFFRACTION3( CHAIN A AND RESID 243:317 )A243 - 317
4X-RAY DIFFRACTION4( CHAIN A AND RESID 318:424 )A318 - 424
5X-RAY DIFFRACTION5( CHAIN A AND RESID 425:522 )A425 - 522
6X-RAY DIFFRACTION6( CHAIN A AND RESID 523:553 )A523 - 553
7X-RAY DIFFRACTION7( CHAIN A AND RESID 554:649 )A554 - 649
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:5 )B1 - 5
9X-RAY DIFFRACTION9( CHAIN B AND RESID 6:11 )B6 - 11

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