[English] 日本語
Yorodumi
- PDB-6mi5: NMR solution structure of lanmodulin (LanM) complexed with yttriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mi5
TitleNMR solution structure of lanmodulin (LanM) complexed with yttrium(III) ions
ComponentsLanmodulin
KeywordsMETAL BINDING PROTEIN / lanthanide / EF-hand / methylotroph / periplasm
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
EF hand / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
YTTRIUM (III) ION / Uncharacterized protein
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCook, E.C. / Featherson, E.R. / Showalter, S.A. / Cotruvo Jr., J.A.
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis for Rare Earth Element Recognition by Methylobacterium extorquens Lanmodulin.
Authors: Cook, E.C. / Featherston, E.R. / Showalter, S.A. / Cotruvo Jr., J.A.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references
Category: pdbx_database_related / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Lanmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7964
Polymers12,5301
Non-polymers2673
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 12structures with acceptable covalent geometry
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Lanmodulin


Mass: 12529.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: MexAM1_META1p1786 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5B164
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-15N NOESY
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D (H)CCH-TOCSY
182isotropic13D H(CCO)NH
191isotropic12D 1H-15N HSQC
1102isotropic12D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.14 mM [U-99% 13C; U-99% 15N] Lanmodulin, 90% H2O/10% D2O5.56mM YCl315N_13C_Sample190% H2O/10% D2O
solution21.26 mM [U-99% 13C; U-99% 15N] Lanmodulin, 90% H2O/10% D2O6.04mM YCl315N_13C_Sample290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.14 mMLanmodulin[U-99% 13C; U-99% 15N]1
1.26 mMLanmodulin[U-99% 13C; U-99% 15N]2
Sample conditionsDetails: 1mM EGTA 20mM MOPS 5mM acetic acid 20mM KCl / Ionic strength: 46mM mM / Ionic strength err: 2 / Label: Condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
SparkyGoddardpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: NOE and TALOS restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 12 / Conformers submitted total number: 12

+
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