[English] 日本語
Yorodumi
- PDB-9p48: Treponema denticola OppA complexed with LSLNSS and SAKASA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p48
TitleTreponema denticola OppA complexed with LSLNSS and SAKASA
Components
  • LEU-SER-LEU-ASN-SER-SER
  • Peptide ABC transporter, peptide-binding protein OppA
  • SER-ALA-LYS-ALA-SER-ALA
KeywordsPEPTIDE BINDING PROTEIN / Oligopeptide permease / OppABCDF / OppA
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
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
Peptide ABC transporter, peptide-binding protein OppA
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsNagy, B.G. / Suits, M.D.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-05457 Canada
CitationJournal: To Be Published
Title: The structure of a Treponema denticola oligopeptide-binding protein A, and peptide compositional preference
Authors: Nagy, B.G. / Suits, M.D.L.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide ABC transporter, peptide-binding protein OppA
B: LEU-SER-LEU-ASN-SER-SER
C: Peptide ABC transporter, peptide-binding protein OppA
D: SER-ALA-LYS-ALA-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,19610
Polymers128,8394
Non-polymers3576
Water4,756264
1
A: Peptide ABC transporter, peptide-binding protein OppA
B: LEU-SER-LEU-ASN-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5814
Polymers64,4622
Non-polymers1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-21 kcal/mol
Surface area22530 Å2
MethodPISA
2
C: Peptide ABC transporter, peptide-binding protein OppA
D: SER-ALA-LYS-ALA-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6156
Polymers64,3772
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-41 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.290, 50.950, 112.000
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein Peptide ABC transporter, peptide-binding protein OppA


Mass: 63842.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: oppA, TDE_1071 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73NT1

-
Protein/peptide , 2 types, 2 molecules BD

#2: Protein/peptide LEU-SER-LEU-ASN-SER-SER


Mass: 619.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide SER-ALA-LYS-ALA-SER-ALA


Mass: 534.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 3 types, 270 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: Tetragonal prisms, clustered
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium iodide, 20% (w/v) PEG3350, 20 mg/mL TdOppA, supplemented with 40 mg/mL DKEVMGILSTALRSMLLTGRDEHGDE (SAR) peptide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.87→45.93 Å / Num. obs: 97540 / % possible obs: 99.88 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.09806 / Rpim(I) all: 0.0409 / Rrim(I) all: 0.1064 / Net I/σ(I): 10.14
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 5.7 % / Num. unique obs: 9574 / CC1/2: 0.142 / CC star: 0.499 / % possible all: 99.62

-
Processing

Software
NameVersionClassification
MxDCdata collection
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→45.93 Å / SU B: 12.339 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24163 4811 4.9 %RANDOM
Rwork0.20729 ---
obs0.20891 92735 99.91 %-
Displacement parametersBiso mean: 27.401 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å2-0 Å2-0.58 Å2
2--0.45 Å2-0 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.87→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9116 0 18 264 9398

+
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