[English] 日本語
Yorodumi
- PDB-2l3m: Solution structure of the putative copper-ion-binding protein fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l3m
TitleSolution structure of the putative copper-ion-binding protein from Bacillus anthracis str. Ames
ComponentsCopper-ion-binding protein
KeywordsMETAL BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


copper ion transport / copper ion binding
Similarity search - Function
Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Copper chaperone / Copper-ion-binding protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsZhang, Y. / Winsor, J. / Dubrovska, I. / Anderson, W. / Radhakrishnan, I. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: To be published
Authors: Zhang, Y. / Winsor, J. / Dubrovska, I. / Anderson, W. / Radhakrishnan, I. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 16, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper-ion-binding protein


Theoretical massNumber of molelcules
Total (without water)7,5831
Polymers7,5831
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 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Copper-ion-binding protein


Mass: 7583.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS3576, BA_3860, GBAA3860, GBAA_3860 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81WV5, UniProt: A0A6H3AJY5*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D 1H-15N NOESY
1523D (H)CCH-TOCSY
1623D 1H-13C NOESY
1723D (H)CCH-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium phosphate, 100 mM sodium chloride, 1 mM beta-mercaptoethanol, 1 mM EDTA, trace mM Protease Inhibitors, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
220 mM potassium phosphate, 100 mM sodium chloride, 1 mM beta-mercaptoethanol, 1 mM EDTA, trace mM Protease Inhibitors, 1 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentSolution-ID
20 mMpotassium phosphate-11
100 mMsodium chloride-21
1 mMbeta-mercaptoethanol-31
1 mMEDTA-41
mMProtease Inhibitors-51
1 mMsodium azide-61
20 mMpotassium phosphate-72
100 mMsodium chloride-82
1 mMbeta-mercaptoethanol-92
1 mMEDTA-102
mMProtease Inhibitors-112
1 mMsodium azide-122
Sample conditionsIonic strength: 0.12 / pH: 6.9 / Pressure: ambient / Temperature: 15 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / 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://pdbjlvh1.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