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

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Basic information

Entry
Database: PDB / ID: 8qlj
TitleCrystal structure of the pneumococcal Substrate-binding protein AliB in complex with an unknown peptide
Components
  • ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • 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 / 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
Oligopeptide-binding protein AliB
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: To Be Published
Title: Crystal structure of the pneumococcal Substrate-binding protein AliB in complex with an unknown peptide
Authors: Alcorlo, M. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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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-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Theoretical massNumber of molelcules
Total (without water)70,8002
Polymers70,8002
Non-polymers00
Water12,647702
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area24760 Å2
Unit cell
Length a, b, c (Å)49.433, 113.458, 58.729
Angle α, β, γ (deg.)90.000, 107.520, 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.: 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-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 44.65 %
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: Sep 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→43.532 Å / Num. obs: 72522 / % possible obs: 98.1 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.1
Reflection shellResolution: 1.65→1.7 Å / Rmerge(I) obs: 0.704 / Num. unique obs: 3496 / CC1/2: 0.99

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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: 1.65→43.532 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 3672 5.07 %
Rwork0.1555 68763 -
obs0.1572 72435 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 23.0406 Å2 / Biso min: 9.68 Å2
Refinement stepCycle: final / Resolution: 1.65→43.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 0 702 5663
Biso mean---35.18 -
Num. residues----630
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.67170.24041320.2159260497
1.6717-1.69460.26671430.2132256396
1.6946-1.71890.22761420.1905262898
1.7189-1.74450.25651400.1895259397
1.7445-1.77180.20541570.1828263798
1.7718-1.80080.23661310.1796258697
1.8008-1.83190.23371420.1701268597
1.8319-1.86520.19671310.1708257297
1.8652-1.90110.22611550.1688267297
1.9011-1.93990.23311400.1711257898
1.9399-1.9820.23341620.1613265398
1.982-2.02820.17991450.1532262297
2.0282-2.07890.17981560.1507261398
2.0789-2.13510.2031440.1483263798
2.1351-2.19790.20081290.1427263698
2.1979-2.26880.18681580.1513264698
2.2688-2.34990.19751410.1572269398
2.3499-2.4440.17671450.1576262899
2.444-2.55520.20861490.1644267099
2.5552-2.68990.20141510.1619265999
2.6899-2.85840.18131360.1554266099
2.8584-3.07910.18071210.1476273099
3.0791-3.38880.1791380.1475264899
3.3888-3.87890.14111280.1352267798
3.8789-4.8860.17381380.1356271499
4.886-43.5320.17831180.1667275999
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)
10.5136-0.81130.64211.843-2.05032.9746-0.1386-0.07270.07410.258-0.0311-0.1762-0.26720.03930.18340.1461-0.031-0.0130.1662-0.01410.162936.118848.195362.3488
20.57580.08710.12861.3245-0.010.7391-0.01450.04850.0235-0.0627-0.00070.0367-0.0901-0.00230.0180.1118-0.01330.00320.11920.00690.104729.550557.038340.8435
30.40.06060.21530.46-0.21280.6280.02510.0271-0.1198-0.0214-0.0244-0.09260.04160.0781-0.01380.11590.00010.01290.15-0.01550.166534.190933.764350.5352
40.19650.3967-0.00492.1971.2541.1255-0.13290.1006-0.1292-0.2283-0.01340.2333-0.0684-0.23910.16510.1886-0.0390.04530.1393-0.03290.157824.802247.081954.0848
50.51850.22150.33850.47280.250.92020.0042-0.0224-0.04660.00260.00360.02660.0529-0.0621-0.00640.1089-0.00830.00140.12480.00280.138914.679431.37149.9865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 274 through 306 )A274 - 306
2X-RAY DIFFRACTION2chain 'A' and (resid 307 through 556 )A307 - 556
3X-RAY DIFFRACTION3chain 'A' and (resid 557 through 652 )A557 - 652
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 9 )B1 - 9
5X-RAY DIFFRACTION5chain 'A' and (resid 32 through 273 )A32 - 273

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