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 

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This is version 2.1 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: https://doi.org/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. 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. [email protected]


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEA,
E [auth G]		566Cereibacter sphaeroidesMutation(s): 0 
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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UniProt GroupP33517
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEB,
F [auth H]		264Cereibacter sphaeroidesMutation(s): 0 
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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UniProt GroupQ03736
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEC,
G [auth I]		266Cereibacter sphaeroidesMutation(s): 0 
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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UniProt GroupP84153
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASED,
H [auth J]		51Cereibacter sphaeroidesMutation(s): 0 
EC: 1.9.3.1
UniProt
Find proteins for Q8KRK5 (Cereibacter sphaeroides)
Explore Q8KRK5 
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UniProt GroupQ8KRK5
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA
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L [auth A],
M [auth A],
Y [auth G],
Z [auth G]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
3PE
Query on 3PE
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AA [auth G]
BA [auth G]
EA [auth I]
FA [auth I]
GA [auth I]
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
CU
Query on CU
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CA [auth H]
DA [auth H]
I [auth A]
P [auth B]
Q [auth B]
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
CA
Query on CA
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K [auth A],
X [auth G]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG
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J [auth A],
W [auth G]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary