1M56

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.

Svensson-Ek, M.Abramson, J.Larsson, G.Tornroth, S.Brzezinski, P.Iwata, S.

(2002) J Mol Biol 321: 329-339

  • DOI: 10.1016/s0022-2836(02)00619-8
  • Primary Citation of Related Structures:  
    1M56, 1M57

  • PubMed Abstract: 
  • The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures ...

    The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures. A comparative study of the wild-type and the EQ(I-286) mutant enzyme revealed structural rearrangements around E(I-286) that could be crucial for proton transfer in this enzyme. In the structure of the mutant enzyme, EQ(I-286), which cannot transfer protons during oxygen reduction, the side-chain of Q(I-286) does not have the hydrogen bond to the carbonyl oxygen of M(I-107) that is seen in the wild-type structure. Furthermore, the Q(I-286) mutant has a different arrangement of water molecules and residues in the vicinity of the Q side-chain. These differences between the structures could reflect conformational changes that take place upon deprotonation of E(I-286) during turnover of the wild-type enzyme, which could be part of the proton-pumping machinery of the enzyme.


    Organizational Affiliation

    Department of Biochemistry, Biomedical Center, Uppsala University, Box 576, Uppsala, Sweden. margareta.e.ek@astrazeneca.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEA, E [auth G]566Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P33517 (Cereibacter sphaeroides)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEB, F [auth H]264Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaCcoxIIctaB
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q03736 (Cereibacter sphaeroides)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEC, G [auth I]266Cereibacter sphaeroidesMutation(s): 0 
Gene Names: EBL86_02290
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P84153 (Cereibacter sphaeroides)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASED, H [auth J]51Cereibacter sphaeroidesMutation(s): 0 
Gene Names: coxIV
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8KRK5 (Cereibacter sphaeroides)
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Go to UniProtKB:  Q8KRK5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA (Subject of Investigation/LOI)
Query on HEA

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], Y [auth G], Z [auth G]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
3PE (Subject of Investigation/LOI)
Query on 3PE

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AA [auth G] , BA [auth G] , EA [auth I] , FA [auth I] , GA [auth I] , HA [auth J] , N [auth A] , O [auth A] , 
AA [auth G], BA [auth G], EA [auth I], FA [auth I], GA [auth I], HA [auth J], N [auth A], O [auth A], R [auth C], S [auth C], T [auth C], U [auth D]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
CA [auth H], DA [auth H], I [auth A], P [auth B], Q [auth B], V [auth G]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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K [auth A], X [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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J [auth A], W [auth G]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 340.36α = 90
b = 340.36β = 90
c = 89.668γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-06-30
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary