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- PDB-2n91: A key amino acid in the control of different functional behavior ... -

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Basic information

Entry
Database: PDB / ID: 2n91
TitleA key amino acid in the control of different functional behavior within the triheme cytochrome family from Geobacter sulfurreducens
ComponentsCytochrome C
KeywordsELECTRON TRANSPORT / triheme cytochrome / electron transfer / Geobacter / site-directed mutagenesis / Redox-Bohr
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c7
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDantas, J.M. / Simoes, T. / Bruix, M. / Salgueiro, C.A.
CitationJournal: J.Phys.Chem.B / Year: 2016
Title: Unveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducens.
Authors: Dantas, J.M. / Simoes, T. / Morgado, L. / Caciones, C. / Fernandes, A.P. / Silva, M.A. / Bruix, M. / Pokkuluri, P.R. / Salgueiro, C.A.
History
DepositionNov 2, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6324
Polymers7,7821
Non-polymers1,8493
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome C / / PpcA


Mass: 7782.166 Da / Num. of mol.: 1 / Fragment: UNP residues 21-91 / Mutation: L6F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: ppcA, RW64_12645 / Plasmid: pCK32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GGK7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM L6F polypeptide, 3 mM PROTOPORPHYRIN IX CONTAINING FE, 45 mM sodium phosphate, 0.04 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.4 mM [U-100% 15N] L6F polypeptide, 3 mM PROTOPORPHYRIN IX CONTAINING FE, 45 mM sodium phosphate, 0.04 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mML6F polypeptide-11
3 mMPROTOPORPHYRIN IX CONTAINING FE-21
45 mMsodium phosphate-31
0.04 %sodium azide-41
0.4 mML6F polypeptide-5[U-100% 15N]2
3 mMPROTOPORPHYRIN IX CONTAINING FE-62
45 mMsodium phosphate-72
0.04 %sodium azide-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 7.1 ambient 298 K
245 7.1 ambient 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospinprocessing
TOPSPINBruker Biospincollection
SPARKYGoddardchemical shift assignment
PARADYANATurner, D. L. Brennan, L. Chamberlin, S. G. Louro, R. O. Xavier, A. V.chemical shift calculation
PARADYANATurner, D. L. Brennan, L. Chamberlin, S. G. Louro, R. O. Xavier, A. V.refinement
MolmolKoradi, Billeter and Wuthrichsuperimposition
MolmolKoradi, Billeter and Wuthrichvisual inspection
CINGNabuurs, Spronk, Krieger, Maassen, Vriend and Vuistervalidation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2398 / NOE intraresidue total count: 769 / NOE long range total count: 586 / NOE medium range total count: 504 / NOE sequential total count: 539
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.25 Å / Maximum upper distance constraint violation: 0.23 Å
NMR ensemble rmsDistance rms dev: 0.96 Å / Distance rms dev error: 0.09 Å

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