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- PDB-2n3b: Structure of oxidized horse heart cytochrome c encapsulated in re... -

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Basic information

Entry
Database: PDB / ID: 2n3b
TitleStructure of oxidized horse heart cytochrome c encapsulated in reverse micelles
ComponentsCytochrome c
KeywordsELECTRON 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 / respirasome / 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 / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model9
AuthorsO'Brien, E.S. / Nucci, N.V. / Fuglestad, B. / Tommos, C. / Wand, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Defining the Apoptotic Trigger: THE INTERACTION OF CYTOCHROME c AND CARDIOLIPIN.
Authors: O'Brien, E.S. / Nucci, N.V. / Fuglestad, B. / Tommos, C. / Wand, A.J.
History
DepositionMay 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3442
Polymers11,7261
Non-polymers6191
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytochrome c /


Mass: 11725.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P00004
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11014D 1H-15N-13C-1H NOESY
11113D HNCO
11222D 1H-15N HSQC
11322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.15 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 pentaneDeuterated pentane
20.15 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 pentaneDeuterated pentane
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.15 mMentity_1-1[U-100% 13C; U-100% 15N]1
1.5 MH2O-21
25 mMsodium phosphate-31
105 mM1-decanoyl-rac-glycerol-41
45 mMlauryldimethylamine-N-oxide-51
8 mMhexanol-61
8.67 Mpentane-7[U-99% 2H]1
0.15 mMentity_1-15[U-100% 15N]2
1.5 MH2O-162
25 mMsodium phosphate-172
105 mM1-decanoyl-rac-glycerol-182
45 mMlauryldimethylamine-N-oxide-192
8 mMhexanol-202
8.67 Mpentane-21[U-99% 2H]2
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddardpeak picking
SPARKYGoddarddata analysis
TOPSPINBruker Biospincollection
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE 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 representativeSelection criteria: closest to the average
NMR ensembleConformer 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 rmsDistance rms dev: 0.0302 Å

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