[English] 日本語
Yorodumi
- PDB-8a42: Crystal structure of the pneumococcal Substrate-binding protein A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a42
TitleCrystal structure of the pneumococcal Substrate-binding protein AmiA in complex with an unknown peptide
Components
  • Oligopeptide-binding protein AmiA
  • Unknown peptide
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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 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
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligopeptide-binding protein AmiA
G: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)71,2632
Polymers71,2632
Non-polymers00
Water12,124673
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.598, 102.702, 107.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Oligopeptide-binding protein AmiA


Mass: 70394.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: amiA, SP_1891 / Production host: Escherichia coli (E. coli) / References: UniProt: P18791
#2: Protein/peptide Unknown peptide


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM Amonium Sulfate and 20% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→47.645 Å / Num. obs: 97923 / % possible obs: 97.2 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.026 / Net I/σ(I): 18.9
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.549 / Num. unique obs: 4649 / CC1/2: 0.84 / Rpim(I) all: 0.218

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→47.645 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 4748 4.85 %
Rwork0.1563 93106 -
obs0.1574 97854 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.49 Å2 / Biso mean: 17.5117 Å2 / Biso min: 5.53 Å2
Refinement stepCycle: final / Resolution: 1.5→47.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 0 673 5628
Biso mean---32.04 -
Num. residues----637
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.5170.26541580.2228295994
1.517-1.53490.22721610.1948299495
1.5349-1.55360.20391930.1865296896
1.5536-1.57330.20771640.1855302395
1.5733-1.5940.22231670.1798298795
1.594-1.61580.22581490.1732300994
1.6158-1.63890.18741470.1722301895
1.6389-1.66340.16691540.1687299694
1.6634-1.68940.21681600.1714303696
1.6894-1.71710.17731720.1587308097
1.7171-1.74670.21281560.1554307198
1.7467-1.77840.17231510.1552313498
1.7784-1.81260.18431540.1548308797
1.8126-1.84960.18911410.1531314398
1.8496-1.88990.21161520.1599296093
1.8899-1.93380.20111650.1586313199
1.9338-1.98220.17731390.1562314699
1.9822-2.03580.18161530.15313798
2.0358-2.09570.18251490.1509317998
2.0957-2.16330.14551650.1482312499
2.1633-2.24070.17951780.1422314999
2.2407-2.33040.16261800.1518314399
2.3304-2.43640.18591470.1572320299
2.4364-2.56490.19971510.1672320199
2.5649-2.72550.17251470.16299394
2.7255-2.9360.16121480.1548323999
2.936-3.23140.16231250.1523326399
3.2314-3.69880.17011810.1393323399
3.6988-4.65950.1361750.134325999
4.6595-47.6450.18941660.1733324294
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)
10.61310.1840.00170.38390.19730.9836-0.0203-0.0014-0.076-0.0236-0.0264-0.03190.12910.0460.01960.08040.01930.01870.05450.00630.081546.374561.873417.1242
20.63080.0731-0.15310.2595-0.2490.81020.0059-0.0552-0.01110.00050.01120.00750.0786-0.1059-0.00850.06340.0001-0.00450.0801-0.00380.080324.520366.020534.3138
30.3510.0123-0.12560.1352-0.1820.6366-0.0312-0.00160.0901-0.179-0.0211-0.0045-0.2181-0.06520.00610.15350.0314-0.0290.0868-0.01570.124141.755280.377313.5011
42.81654.1795-0.68746.4516-1.30050.48330.3434-0.49590.48940.5779-0.31670.0413-0.17860.2514-0.02590.15680.01170.02720.2318-0.05470.18539.194168.213732.4478
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 601 )A291 - 601
3X-RAY DIFFRACTION3chain 'A' and (resid 602 through 659 )A602 - 659
4X-RAY DIFFRACTION4chain 'G' and (resid 1 through 10 )G1 - 10

+
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