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- PDB-8qm0: Crystal structure of the pneumococcal Substrate-binding protein A... -

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Basic information

Entry
Database: PDB / ID: 8qm0
TitleCrystal structure of the pneumococcal Substrate-binding protein AmiA in complex with Peptide 5
Components
  • ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG
  • Oligopeptide-binding protein AmiA
KeywordsPEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AmiA / 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 AmiA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Bacteria (eubacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 AmiA
B: Oligopeptide-binding protein AmiA
C: Oligopeptide-binding protein AmiA
D: Oligopeptide-binding protein AmiA
E: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG
F: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG
G: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG
H: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Theoretical massNumber of molelcules
Total (without water)286,2278
Polymers286,2278
Non-polymers00
Water37,2552068
1
A: Oligopeptide-binding protein AmiA
E: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Theoretical massNumber of molelcules
Total (without water)71,5572
Polymers71,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-2 kcal/mol
Surface area23490 Å2
MethodPISA
2
B: Oligopeptide-binding protein AmiA
F: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Theoretical massNumber of molelcules
Total (without water)71,5572
Polymers71,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-3 kcal/mol
Surface area23480 Å2
MethodPISA
3
C: Oligopeptide-binding protein AmiA
G: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Theoretical massNumber of molelcules
Total (without water)71,5572
Polymers71,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area23700 Å2
MethodPISA
4
D: Oligopeptide-binding protein AmiA
H: ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Theoretical massNumber of molelcules
Total (without water)71,5572
Polymers71,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-5 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.651, 206.756, 96.795
Angle α, β, γ (deg.)90.000, 90.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oligopeptide-binding protein AmiA


Mass: 70394.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: amiA, SP_1891 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18791
#2: Protein/peptide
ALA-LYS-THR-ILE-LYS-ILE-THR-GLN-THR-ARG


Mass: 1162.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bacteria (eubacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2068 / 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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric Acid and 25% PEG3350

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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: 1.76→49.173 Å / Num. obs: 213511 / % possible obs: 97.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.7
Reflection shellResolution: 1.76→1.82 Å / Num. unique obs: 10351 / CC1/2: 0.79

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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: 1.76→49.173 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 10605 4.97 %
Rwork0.1565 202715 -
obs0.1586 213320 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.59 Å2 / Biso mean: 27.4344 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 1.76→49.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19940 0 0 2068 22008
Biso mean---37.16 -
Num. residues----2548
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.76-1.780.39033000.3107660295
1.78-1.80090.3433130.2893671097
1.8009-1.82290.30783420.2524664695
1.8229-1.8460.29393610.2313662797
1.846-1.87030.27863600.2193667696
1.8703-1.89590.26263270.2024670796
1.8959-1.9230.26073540.1877667697
1.923-1.95170.23413530.1751669295
1.9517-1.98220.21463580.1655669498
1.9822-2.01470.21853430.1669671996
2.0147-2.04940.23113530.1692670097
2.0494-2.08670.22053600.1683670797
2.0867-2.12680.20383260.1635672897
2.1268-2.17020.2153720.1654675097
2.1702-2.21740.21633700.167672498
2.2174-2.2690.19813570.1547674197
2.269-2.32580.19713280.1529680198
2.3258-2.38860.20883780.1565673497
2.3886-2.45890.2143460.1591681397
2.4589-2.53830.22053670.1576676998
2.5383-2.6290.1973220.1566683898
2.629-2.73430.21743260.1564680498
2.7343-2.85870.19133840.1466683598
2.8587-3.00940.1843740.1474681298
3.0094-3.19790.18593300.1467686099
3.1979-3.44470.18773990.1428683399
3.4447-3.79130.1583690.1315687799
3.7913-4.33960.15663630.1223689399
4.3396-5.46630.16493990.1343687199
5.4663-49.1730.18193710.1663687698
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)
11.0973-0.48820.08051.2226-0.1420.66680.0530.04540.1093-0.0421-0.0692-0.1436-0.1140.10290.01580.1599-0.01450.01440.16550.01880.12537.0319-32.499145.9441
21.170.0677-0.32810.6817-0.11540.253-0.1210.1393-0.1169-0.0678-0.04330.15340.0816-0.03570.11640.15240.00430.02330.1761-0.01470.17216.6522-55.85542.687
31.2371-0.02-0.43680.68820.11520.789-0.06680.0393-0.2306-0.01870.01860.04330.121-0.01980.04570.1547-0.00110.00340.16660.0090.182214.9985-54.371647.3245
41.1140.11690.09860.96150.04440.68360.02850.1055-0.0023-0.11970.0180.2222-0.0831-0.0558-0.04630.15620.00930.00550.1830.02520.169214.3147-39.864845.1542
50.805-0.0258-0.14070.8974-0.53690.9813-0.1056-0.37130.04280.51760.09620.051-0.14450.0240.0140.33340.04710.02380.2869-0.0220.159232.1927-33.526864.6248
61.4138-0.09520.08381.43070.26440.65760.01770.08030.2191-0.1483-0.06060.085-0.07840.01270.04140.1222-0.0083-0.00950.1271-0.0010.120233.763-27.392691.8432
71.0318-0.01050.18760.8985-0.17841.12840.0791-0.1621-0.18180.04640.0081-0.05350.1872-0.0442-0.07720.1477-0.0202-0.03010.21120.02580.155239.9984-50.2673105.1782
81.17970.0142-0.20390.98540.060.09390.02070.047-0.1559-0.1124-0.06120.14160.0207-0.04850.03910.1343-0.0085-0.00960.1512-0.01580.151414.5373-55.45890.2018
91.5737-0.7833-0.03212.74820.29761.1889-0.0408-0.40310.0030.22030.04480.02480.06910.0378-0.03060.1297-0.03470.00770.2516-0.01390.123215.2697-49.0668105.7694
101.3453-0.2696-0.15470.80780.22490.50630.02940.0066-0.1756-0.0578-0.02590.13120.0924-0.0151-0.01110.145-0.0097-0.02920.1375-0.01710.156912.3264-55.525191.655
111.43740.38120.40780.91160.09350.89420.0142-0.00480.2047-0.1331-0.03650.2295-0.0539-0.05620.02570.1241-0.0058-0.01070.1416-0.01450.193312.2194-39.545493.3581
121.0017-0.08710.26041.0413-0.00230.71580.0063-0.30570.03860.28150.00470.0144-0.0111-0.0783-0.01560.2179-0.02360.02570.2624-0.02610.151130.0156-34.8709113.2159
131.50320.6470.06731.5134-0.01550.54050.0156-0.2031-0.22240.0805-0.0569-0.04930.07710.01580.03560.1430.02330.00890.14870.02760.117260.4471-110.803878.376
141.20830.0224-0.0161.3482-0.34020.9587-0.06840.00590.08950.02550.0359-0.1571-0.09440.05610.03270.1242-0.0158-0.00520.1478-0.01730.115670.1778-90.770768.9971
151.0211-0.02680.24430.8043-0.01560.1401-0.166-0.25540.24760.08030.07340.12-0.0196-0.04780.09010.16660.0516-0.04310.1831-0.06290.183543.0372-80.635878.4589
161.8776-0.06950.5610.95290.20360.784-0.131-0.11880.12350.05850.08260.1258-0.0745-0.03460.02570.1210.02380.00730.1337-0.00670.133240.7278-86.35376.3352
170.9292-0.4429-0.35810.4688-0.01990.55090.0110.0019-0.0334-0.02020.00620.139-0.0772-0.0135-0.00440.13-0.0101-0.03320.1337-0.00130.160944.1954-94.399267.8235
180.2382-0.195-0.04211.3203-0.61041.109-0.03380.08590.0051-0.41980.02370.24550.14720.0250.01010.2527-0.0218-0.03670.1686-0.00070.177758.6324-102.793956.638
191.4357-0.5056-0.08072.1237-0.34370.46290.05780.0804-0.22360.0043-0.07350.19020.03360.06260.00020.13860.013-0.01310.1553-0.02360.133465.0098-104.120725.9764
201.3177-0.17740.45671.1258-0.25820.2451-0.0329-0.05330.05940.1066-0.02840.1556-0.03640.01360.00690.15410.00920.0080.13760.01670.152544.4123-81.146731.3482
211.7698-0.18630.22081.00380.1210.62460.01850.10530.01650.00990.03830.1516-0.0925-0.028-0.05850.1470.00460.01880.14550.02030.145242.9041-82.318526.4309
221.2981-0.8392-0.15151.1577-0.07090.9880.00970.0051-0.42970.11080.03640.43930.1007-0.0676-0.020.1471-0.00180.00540.1540.01910.328842.1439-97.02227.4985
230.9049-0.55790.04220.64650.00520.57420.33160.6182-0.1203-0.4716-0.18990.28180.09760.0387-0.03430.3440.0948-0.11170.3641-0.0590.229259.6875-101.52487.5708
243.2516-1.95022.45192.9281-2.9174.29420.1819-0.3142-0.88840.1034-0.2671-0.19480.2920.25090.05750.332-0.0426-0.06010.28920.06660.440929.8725-48.870748.5224
252.7222-1.30462.46371.8697-2.93464.71080.0697-0.1362-0.504-0.1297-0.10830.19510.37810.25940.11580.2712-0.00070.01830.2569-0.04960.354627.7456-49.147996.2665
263.0811.8671-2.4623.0322-1.32754.8073-0.15840.18020.8230.01150.06710.0082-0.4030.21530.05720.26010.0007-0.05230.2537-0.00550.379756.5369-87.658672.8167
272.6472.0492-2.60923.4075-2.86665.21930.12620.29670.4961-0.0117-0.2179-0.016-0.31050.25220.06040.34850.0399-0.05990.31060.0170.379857.6695-87.602324.8471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 290 )A33 - 290
2X-RAY DIFFRACTION2chain 'A' and (resid 291 through 346 )A291 - 346
3X-RAY DIFFRACTION3chain 'A' and (resid 347 through 510 )A347 - 510
4X-RAY DIFFRACTION4chain 'A' and (resid 511 through 601 )A511 - 601
5X-RAY DIFFRACTION5chain 'A' and (resid 602 through 659 )A602 - 659
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 235 )B33 - 235
7X-RAY DIFFRACTION7chain 'B' and (resid 236 through 290 )B236 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 348 )B291 - 348
9X-RAY DIFFRACTION9chain 'B' and (resid 349 through 382 )B349 - 382
10X-RAY DIFFRACTION10chain 'B' and (resid 383 through 510 )B383 - 510
11X-RAY DIFFRACTION11chain 'B' and (resid 511 through 601 )B511 - 601
12X-RAY DIFFRACTION12chain 'B' and (resid 602 through 659 )B602 - 659
13X-RAY DIFFRACTION13chain 'C' and (resid 33 through 204 )C33 - 204
14X-RAY DIFFRACTION14chain 'C' and (resid 205 through 290 )C205 - 290
15X-RAY DIFFRACTION15chain 'C' and (resid 291 through 348 )C291 - 348
16X-RAY DIFFRACTION16chain 'C' and (resid 349 through 561 )C349 - 561
17X-RAY DIFFRACTION17chain 'C' and (resid 562 through 601 )C562 - 601
18X-RAY DIFFRACTION18chain 'C' and (resid 602 through 659 )C602 - 659
19X-RAY DIFFRACTION19chain 'D' and (resid 33 through 290 )D33 - 290
20X-RAY DIFFRACTION20chain 'D' and (resid 291 through 346 )D291 - 346
21X-RAY DIFFRACTION21chain 'D' and (resid 347 through 510 )D347 - 510
22X-RAY DIFFRACTION22chain 'D' and (resid 511 through 601 )D511 - 601
23X-RAY DIFFRACTION23chain 'D' and (resid 602 through 659 )D602 - 659
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 10 )E1 - 10
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 10 )F1 - 10
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 10 )G1 - 10
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 10 )H1 - 10

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