[English] 日本語
Yorodumi
- PDB-8qlm: Crystal structure of the pneumococcal Substrate-binding protein A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qlm
TitleCrystal structure of the pneumococcal Substrate-binding protein AliB in complex with Peptide 3
Components
  • Oligopeptide-binding protein AliB
  • PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 Peptide 3
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligopeptide-binding protein AliB
B: Oligopeptide-binding protein AliB
C: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL
D: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)142,0194
Polymers142,0194
Non-polymers00
Water22,6631258
1
A: Oligopeptide-binding protein AliB
C: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)71,0102
Polymers71,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-10 kcal/mol
Surface area24360 Å2
2
B: Oligopeptide-binding protein AliB
D: PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)71,0102
Polymers71,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area24410 Å2
Unit cell
Length a, b, c (Å)64.204, 108.837, 86.643
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Oligopeptide-binding protein AliB


Mass: 70016.430 Da / Num. of mol.: 2
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 PRO-ILE-VAL-GLY-GLY-HIS-GLU-GLY-ALA-GLY-VAL


Mass: 993.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1258 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium Acetate, 8% 2-Propanol and 21% PEG4000

-
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: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.66→47.02 Å / Num. obs: 134554 / % possible obs: 97.6 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.9
Reflection shellResolution: 1.66→1.71 Å / Rmerge(I) obs: 0.792 / Num. unique obs: 6595 / CC1/2: 0.77

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→47.02 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 6737 5.01 %
Rwork0.1663 127738 -
obs0.1683 134475 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.11 Å2 / Biso mean: 29.3002 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.66→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9970 0 0 1258 11228
Biso mean---37.08 -
Num. residues----1264
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.66-1.67890.29732170.2573419896
1.6789-1.69860.31122420.2451417696
1.6986-1.71930.2742150.2341418096
1.7193-1.74110.26082180.2238418896
1.7411-1.7640.28072310.2148417796
1.764-1.78820.262530.214420596
1.7882-1.81370.26112360.2064416796
1.8137-1.84080.26952310.1969419497
1.8408-1.86960.24112400.1869416697
1.8696-1.90020.23062230.1808423697
1.9002-1.9330.27592310.1925423597
1.933-1.96810.2352390.1845422297
1.9681-2.0060.22262140.1685428397
2.006-2.04690.23822000.1707423297
2.0469-2.09150.22141920.1693423597
2.0915-2.14010.20472350.1648429397
2.1401-2.19360.18212120.1567420597
2.1936-2.25290.2242300.1648426398
2.2529-2.31920.22592240.1739427798
2.3192-2.39410.23641950.1687428798
2.3941-2.47960.20582210.1696432698
2.4796-2.57890.21282150.1729431398
2.5789-2.69630.19662150.1624427298
2.6963-2.83840.20622260.1648430598
2.8384-3.01620.20192180.1678432399
3.0162-3.24910.20852450.1593433499
3.2491-3.57590.17152120.1481434299
3.5759-4.09310.15312330.1404434799
4.0931-5.15590.16882070.1419438299
5.1559-47.020.19232670.1704437599
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)
11.6647-0.1215-0.15180.9396-0.35290.5603-0.08430.13920.07-0.10480.05410.03950.0168-0.07120.02220.1459-0.0117-0.02490.12850.00880.13676.079526.863929.5459
20.54560.4275-0.16790.7951-0.56740.6213-0.10810.0287-0.1998-0.0913-0.0789-0.34380.1460.1290.15430.17370.01260.03820.15480.03020.297130.123214.379433.4928
30.7491-0.25050.11481.7755-0.34880.5484-0.0164-0.0501-0.12350.0350.03140.03880.0684-0.0495-0.01490.14620.00240.00880.14030.01590.150110.4941.204449.1027
40.92610.2325-0.04750.9737-0.4980.5566-0.0916-0.08540.09070.166-0.039-0.1682-0.09130.03560.12760.16820.0119-0.04240.1321-0.00610.171221.283424.28445.8317
51.86680.05980.09620.80040.07360.7327-0.0624-0.03120.1835-0.1066-0.06920.1229-0.076-0.06550.11250.15130.012-0.02950.137-0.03530.137132.081628.43271.524
62.12270.81770.27081.45080.07630.31910.1166-0.5246-0.44110.1644-0.1631-0.1220.0746-0.02860.04320.2172-0.01210.00730.29050.09290.171540.03567.013885.9454
70.8480.24050.6830.08160.02072.8093-0.04550.5374-0.7297-0.6647-0.2826-0.83470.99791.10220.26890.50860.1450.19140.44460.00410.683318.47197.773337.5656
80.2246-0.2680.61090.7002-1.15872.1467-0.13220.5568-0.5239-0.6697-0.3762-0.80810.99250.86320.4160.63260.02020.32310.5062-0.05440.675942.29988.137577.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 220 )A29 - 220
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 303 )A221 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 553 )A304 - 553
4X-RAY DIFFRACTION4chain 'A' and (resid 554 through 649 )A554 - 649
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 242 )B29 - 242
6X-RAY DIFFRACTION6chain 'B' and (resid 243 through 649 )B243 - 649
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 11 )C1 - 11
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 11 )D1 - 11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more