[English] 日本語
Yorodumi
- PDB-1afi: STRUCTURE OF THE REDUCED FORM OF MERP, THE PERIPLASMIC PROTEIN FR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1afi
TitleSTRUCTURE OF THE REDUCED FORM OF MERP, THE PERIPLASMIC PROTEIN FROM THE BACTERIAL MERCURY DETOXIFICATION SYSTEM, NMR, 20 STRUCTURES
ComponentsMERP
KeywordsMERCURY DETOXIFICATION / PERIPLASMIC / HEAVY METAL TRANSPORT / ALPHA-BETA SANDWICH
Function / homology
Function and homology information


mercury ion transmembrane transporter activity / mercury ion binding / periplasmic space
Similarity search - Function
Mercuric transport protein periplasmic component / Mercuric transport protein periplasmic component/copper chaperone CopZ / 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 ...Mercuric transport protein periplasmic component / Mercuric transport protein periplasmic component/copper chaperone CopZ / 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
Mercuric transport protein periplasmic component
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsSteele, R.A. / Opella, S.J.
CitationJournal: Biochemistry / Year: 1997
Title: Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system.
Authors: Steele, R.A. / Opella, S.J.
History
DepositionMar 7, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MERP


Theoretical massNumber of molelcules
Total (without water)7,4841
Polymers7,4841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80LOWEST ENERGY
Representative

-
Components

#1: Protein MERP / MERCURIC TRANSPORT PROTEIN


Mass: 7483.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN STUDIED EXCLUDES THE PRECURSOR SIGNAL SEQUENCE. THIS IS THE NATIVE FORM OF THE PROTEIN AFTER CELL PROCESSING.
Source: (gene. exp.) Shigella flexneri (bacteria) / Description: MER GENES LOCATED ON TRANSPOSON TN21 / Cellular location: PERIPLASM / Gene: MERP / Plasmid: PSSS / Species (production host): Escherichia coli / Gene (production host): MERP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04129

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HMQC-NOESY
121HMQC-TOCSY
131HNCA
141HN(CO)CA
151CBCA(CO)NH

-
Sample preparation

Sample conditionspH: 6.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DMX750BrukerDMX7507503

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IN SUMMARY, INITIAL CALCULATIONS WERE STARTED FROM A LINEAR POLYPEPTIDE TEMPLATE WITH RANDOM BACKBONE ANGLES. AN ITERATIVE ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IN SUMMARY, INITIAL CALCULATIONS WERE STARTED FROM A LINEAR POLYPEPTIDE TEMPLATE WITH RANDOM BACKBONE ANGLES. AN ITERATIVE REFINEMENT WAS EMPLOYED USING ADDITIONAL RESTRAINTS AS THE QUALITY OF THE STRUCTURES IMPROVED AND AMBIGUITIES IN THE DATA WERE RESOLVED.
NMR ensembleConformer selection criteria: 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://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