5GXG

High-resolution crystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of productive and futile encounters in an electron transfer protein complex

Andraojc, W.Hiruma, Y.Liu, W.M.Ravera, E.Nojiri, M.Parigi, G.Luchinat, C.Ubbink, M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E1840-E1847

  • DOI: 10.1073/pnas.1616813114

  • PubMed Abstract: 
  • Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved re ...

    Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands; luchinat@cerm.unifi.it m.ubbink@chem.leidenuniv.nl.,Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.,RIKEN SPring-8 Center, Hyogo 679-5148, Japan.,Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy.,Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands.,Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; luchinat@cerm.unifi.it m.ubbink@chem.leidenuniv.nl.,Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Camphor 5-monooxygenase
A
416Pseudomonas putidaMutation(s): 3 
Gene Names: camC (cyp101)
EC: 1.14.15.1
Find proteins for P00183 (Pseudomonas putida)
Go to UniProtKB:  P00183
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putidaredoxin
B
108Pseudomonas putidaMutation(s): 0 
Gene Names: camB
Find proteins for P00259 (Pseudomonas putida)
Go to UniProtKB:  P00259
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FES
Query on FES

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Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.490α = 90.00
b = 77.956β = 95.51
c = 59.968γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Data collection, Database references