[English] 日本語
Yorodumi
- PDB-9e9a: Solution structure of an uncharacterized protein containing a DUF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e9a
TitleSolution structure of an uncharacterized protein containing a DUF1893 domain from Borrelia burgdorferi, a pathogen responsible for Lyme disease. Seattle Structural Genomics Center for Infectious Disease target BobuA.17726.a.A1.
ComponentsDUF1893 domain-containing protein
KeywordsUNKNOWN FUNCTION / Lyme disease / DUFs / cytosine deaminase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyProtein of unknown function DUF1893, TM1506-like / Hypothetical protein TM1506 / Domain of unknown function (DUF1893) / Cytidine deaminase-like / catalytic activity / DUF1893 domain-containing protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodSOLUTION NMR / water refinement
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To Be Published
Title: Structural characterization of a DUF1893 domain containing protein from Borrelia burgdorferi, a pathogen responsible for Lyme disease.
Authors: Buchko, G.W. / van Voorhis, W.C. / Myler, P.J.
History
DepositionNov 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF1893 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,0061
Polymers17,0061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography was consistent with a monomer as was a NMR measured tauC. Moreover, at 150 residues poorer NMR data would be expected if it was a dimer ...Evidence: gel filtration, Size exclusion chromatography was consistent with a monomer as was a NMR measured tauC. Moreover, at 150 residues poorer NMR data would be expected if it was a dimer (deuteration would be necessary to make the assignments). One oddity is that it was not possible to assign any of the methyl groups for the 15 leucine residues.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein DUF1893 domain-containing protein


Mass: 17005.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0429 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O51390
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic
1141isotropic13D HN(CA)CB
1131isotropic13D CBCA(CO)NH
1121isotropic13D HCACO
1111isotropic13D HNCO
1101isotropic13D HNCA
191isotropic13D C(CO)NH
181isotropic23D HBHA(CO)NH
171isotropic23D H(CCO)NH
162isotropic22D 1H-15N HSQC
1162isotropic23D 1H-13C NOESY aliphatic
1173isotropic22D 1H-13C HSQC aliphatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11 mM [U-98% 13C; U-98% 15N] B26, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2OCN193% H2O/7% D2O
solution21 mM [U-98% 13C; U-98% 15N] B26, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2OCN293% H2O/7% D2OUsed for the deuterium exchange experiment. Sample was lyophilized and then redissolved into d2o. HSQC collected within 15 min.
solution31 mM [U-10% 13C; U-98% 15N] B26, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2OC10N93% H2O/7% D2OUsed for the deuterium exchange experiment. Sample was lyophilized and then redissolved into d2o. HSQC collected within 15 min.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMB26[U-98% 13C; U-98% 15N]1
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
1 mMB26[U-98% 13C; U-98% 15N]2
100 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance2
1 mMDTTnatural abundance2
1 mMB26[U-10% 13C; U-98% 15N]3
100 mMsodium chloridenatural abundance3
20 mMTRISnatural abundance3
1 mMDTTnatural abundance3
Sample conditionsIonic strength: 120 mM / Label: Con-1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 278 K / Temperature err: 0.5

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Bruker AscendBrukerAscend7002

-
Processing

NMR software
NameVersionDeveloperClassification
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS+Baxrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRtistKlukowski, Riek and Guntertchemical shift assignment
RefinementMethod: water refinement / Software ordinal: 5
Details: STRUCTURE CALCULATIONS WERE PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE CALCULATIONS WERE PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW FOR THE LOWER LIMIT. HYDROGEN BOND RESTRAINTS WERE INTRODUCED ON THE BASIS OF SLOWLY EXCHANGING AMIDE RESONANCES OBSERVED IN THE DEUTERIUM EXCHANGE EXPERIMENT AND PROXIMITY IN EARLY STRUCTURE CALCULATIONS. STERO-ASSIGNMENTS WERE MADE FOR 10/11ON THE BASIS OF 1H-13C HSQC SPECTRUM FOR THE 10%-CARBON-13 LABELLED SAMPLE.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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