[English] 日本語
Yorodumi
- PDB-2kxi: Solution NMR structure of the apoform of NarE (NMB1343) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kxi
TitleSolution NMR structure of the apoform of NarE (NMB1343)
ComponentsUncharacterized protein
KeywordsTRANSFERASE / ADP ribosyltransferase
Function / homology: / NarE / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKoehler, C. / Carlier, L. / Veggi, D. / Soriani, M. / Pizza, M. / Boelens, R. / Bonvin, A.M.J.J.
CitationJournal: To be Published
Title: Solution NMR structure of the apoform of NarE (NMB1343)
Authors: Koehler, C. / Carlier, L. / Veggi, D. / Soriani, M. / Pizza, M. / Boelens, R. / Bonvin, A.M.J.J.
History
DepositionMay 6, 2010Deposition site: BMRB / Processing site: PDBJ
SupersessionMar 2, 2011ID: 2KWR
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2018Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / struct
Item: _entity.pdbx_description / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.type / _struct.pdbx_descriptor

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4291
Polymers17,4291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein / NMB1343


Mass: 17429.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: NMB1343 / Variant: serogroup B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JZ10

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HNCO
1623D HN(CA)CO
1723D HNCA
1823D HBHA(CO)NH
1913D 1H-15N NOESY
11033D 1H-13C NOESY
11133D (H)CCH-TOCSY
11232D 1H-1H TOCSY
11322D 1H-1H NOESY
11412D 1H-15N HSQC T1 edited
11512D 1H-15N HSQC T2 edited
11612D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM [U-100% 15N] NMB1343, 75 mM sodium chloride, 25 mM sodium phosphate, 0.01 % sodium azide, 0.5 mM TSP, 1 mM DTT, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.6 mM [U-100% 13C; U-100% 15N] NMB1343, 75 mM sodium chloride, 25 mM sodium phosphate, 0.01 % sodium azide, 0.5 mM TSP, 1 mM DTT, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.8 mM [U-100% 13C; U-100% 15N] NMB1343, 75 mM sodium chloride, 25 mM sodium phosphate, 0.01 % sodium azide, 0.5 mM TSP, 1 mM DTT, 100% D2Osample_3100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMNMB1343-1[U-100% 15N]1
75 mMsodium chloride-21
25 mMsodium phosphate-31
0.01 %sodium azide-41
0.5 mMTSP-51
1 mMDTT-61
0.6 mMNMB1343-7[U-100% 13C; U-100% 15N]2
75 mMsodium chloride-82
25 mMsodium phosphate-92
0.01 %sodium azide-102
0.5 mMTSP-112
1 mMDTT-122
0.8 mMNMB1343-13[U-100% 13C; U-100% 15N]3
75 mMsodium chloride-143
25 mMsodium phosphate-153
0.01 %sodium azide-163
0.5 mMTSP-173
1 mMDTT-183
Sample conditionsLabel: sample_conditions / pH: 7.3 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Oxford AvanceOxfordAvance7502
Bruker AvanceBrukerAvance6003

-
Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
SPARKYGoddardchemical shift assignment
SPARKYGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 7 / Details: CNS refinement in water
NMR constraintsNOE constraints total: 661 / NOE intraresidue total count: 0 / NOE long range total count: 257 / NOE medium range total count: 139 / NOE sequential total count: 265 / Hydrogen bond constraints total count: 85 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 99 / Protein psi angle constraints total count: 99
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.8 ° / Maximum upper distance constraint violation: 0.36 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.03 Å

+
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