- PDB-2n3b: Structure of oxidized horse heart cytochrome c encapsulated in re... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2n3b
Title
Structure of oxidized horse heart cytochrome c encapsulated in reverse micelles
Components
Cytochrome c
Keywords
ELECTRON TRANSPORT / reverse micelle / structural water / paramagnetic
Function / homology
Function and homology information
cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / lipid binding / apoptotic process / heme binding / identical protein binding / metal ion binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-13C HSQC
1
3
1
3D HNCA
1
4
1
3DHN(CO)CA
1
5
1
3D (H)CCH-TOCSY
1
6
1
3DH(CCO)NH
1
7
1
3DC(CO)NH
1
8
1
3D 1H-15N NOESY
1
9
1
3D 1H-13C NOESY aliphatic
1
10
1
4D 1H-15N-13C-1H NOESY
1
11
1
3D HNCO
1
12
2
2D 1H-15N HSQC
1
13
2
2D 1H-13C HSQC
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.15 mM [U-100% 13C; U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane
Deuteratedpentane
2
0.15 mM [U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane
Deuteratedpentane
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.15mM
entity_1-1
[U-100% 13C; U-100% 15N]
1
1.5M
H2O-2
1
25mM
sodium phosphate-3
1
105mM
1-decanoyl-rac-glycerol-4
1
45mM
lauryldimethylamine-N-oxide-5
1
8mM
hexanol-6
1
8.67M
pentane-7
[U-99% 2H]
1
0.15mM
entity_1-15
[U-100% 15N]
2
1.5M
H2O-16
2
25mM
sodium phosphate-17
2
105mM
1-decanoyl-rac-glycerol-18
2
45mM
lauryldimethylamine-N-oxide-19
2
8mM
hexanol-20
2
8.67M
pentane-21
[U-99% 2H]
2
Sample conditions
pH: 7.4 / Pressure: ambient / Temperature: 298 K
-
NMR measurement
NMR spectrometer
Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz
-
Processing
NMR software
Name
Developer
Classification
Felix
AccelrysSoftwareInc.
processing
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
SPARKY
Goddard
peakpicking
SPARKY
Goddard
dataanalysis
TOPSPIN
BrukerBiospin
collection
X-PLOR_NIH
Schwieters, Kuszewski, TjandraandClore
structuresolution
TALOS
Cornilescu, DelaglioandBax
dataanalysis
X-PLOR_NIH
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
NOE constraints total: 2054 / NOE intraresidue total count: 441 / NOE long range total count: 291 / NOE medium range total count: 280 / NOE sequential total count: 427 / Protein phi angle constraints total count: 72 / Protein psi angle constraints total count: 73
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 32 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 1.917 ° / Maximum upper distance constraint violation: 0.287 Å
NMR ensemble rms
Distance rms dev: 0.0302 Å
+
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