- PDB-2p0b: Crystal structure of chemically-reduced E.coli nrfB -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2p0b
Title
Crystal structure of chemically-reduced E.coli nrfB
Components
Cytochrome c-type protein nrfB
Keywords
ELECTRON TRANSPORT / PENTAHEME C-TYPE CYTOCHROME
Function / homology
Function and homology information
nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / outer membrane-bounded periplasmic space / oxidoreductase activity / electron transfer activity / heme binding / metal ion binding Similarity search - Function
Cytochrome c nitrite reductase, pentahaem subunit / Cytochrome c-552/4 / Cytochrome c554 and c-prime / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal grow
Temperature: 289 K / pH: 7.5 Details: Purified NrfB was concentrated to 8 mg/ml before crystallization. Crystals were obtained by the vapour diffusion method under anaerobic conditions using 250 mM tri-sodium citrate, 10 mM ...Details: Purified NrfB was concentrated to 8 mg/ml before crystallization. Crystals were obtained by the vapour diffusion method under anaerobic conditions using 250 mM tri-sodium citrate, 10 mM Na2S2O4 and 20 % (v/v) isopropanol in 100 mM sodium HEPES pH 7.5. Crystals were soaked in 100 mM Na2S2O4 prior to harvesting, temperature 289K
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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