OXIDOREDUCTASE / ALL BETA-PROTEIN / METALLO-PROTEIN
Function / homology
Function and homology information
mitochondrial cytochrome c oxidase assembly / Mitochondrial protein degradation / : / mitochondrial electron transport, cytochrome c to oxygen / proton transmembrane transport / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / zinc ion binding Similarity search - Function
q5lls5 like domains / HSP40/DNAj peptide-binding domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
1
2D TOCSY
1
3
1
HNHA
1
4
2
3D 13C-separated NOESY
1
5
1
3D 15N-separated NOESY
1
6
2
CBCA(CO)NH
1
7
2
CBCANH
1
8
2
HNCO
1
9
2
HN(CA)CO
1
10
2
(H)CCH-TOCSY
NMR details
Text: The structure was determined using triple-resonance NMR spectroscopy
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM Zn(II)Cox4 U-15N, 50mM phosphate buffer NA, 200 mM NaCl, 90% H2O, 10% D2O
90% H2O/10% D2O
2
1 mM Zn(II)Cox4 U-15N,13C, 50mM phosphate buffer NA, 200 mM NaCl, 90% H2O, 10% D2O
90% H2O/10% D2O
Sample conditions
Ionic strength: 50 mM phosphate, 200 mM NaCl / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
800
1
Bruker AVANCE
Bruker
AVANCE
500
2
Bruker AVANCE
Bruker
AVANCE
700
3
-
Processing
NMR software
Name
Version
Classification
XwinNMR
collection
XwinNMR
processing
CARA
dataanalysis
CYANA
structuresolution
Amber
8
refinement
Refinement
Method: torsion angle dynamics / Software ordinal: 1 Details: Structure calculations were performed with the software package ATNOS/CANDID/CYANA. The structures are based on a total of 1218 restraints, 1172 are NOE-derived distance constraints, 46 are ...Details: Structure calculations were performed with the software package ATNOS/CANDID/CYANA. The structures are based on a total of 1218 restraints, 1172 are NOE-derived distance constraints, 46 are dihedral angle restraints.
NMR representative
Selection criteria: minimized average structure
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 21
+
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.
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