 |
PDBsum entry 4xva
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
4xva
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Oxidoreductase
|
|
|
Title:
|
|
Crystal structure of wild type cytochromE C peroxidase
|
|
Structure:
|
|
CytochromE C peroxidase, mitochondrial. Chain: a, c, e, g. Fragment: unp residues 69-361. Synonym: ccp. Engineered: yes
|
|
Source:
|
|
Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: ccp1, ccp, cpo, ykr066c. Expressed in: escherichia coli. Expression_system_taxid: 469008.
|
|
Resolution:
|
|
|
2.66Å
|
R-factor:
|
0.235
|
R-free:
|
0.276
|
|
|
Authors:
|
|
M.Fischer,J.S.Fraser
|
|
Key ref:
|
|
M.Fischer
et al.
(2015).
One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
Chembiochem,
16,
1560-1564.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
26-Jan-15
|
Release date:
|
25-Feb-15
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P00431
(CCPR_YEAST) -
Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
|
|
|
|
Seq:
Struc:
|
|
|
|
361 a.a.
293 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.1.11.1.5
- cytochrome-c peroxidase.
|
|
|
|
|
|
|
Reaction:
|
|
2 Fe(II)-[cytochrome c] + H2O2 + 2 H+ = 2 Fe(III)-[cytochrome c] + 2 H2O
|
|
|
|
|
|
2
×
Fe(II)-[cytochrome c]
|
+
|
H2O2
|
+
|
2
×
H(+)
|
=
|
2
×
Fe(III)-[cytochrome c]
|
+
|
2
×
H2O
|
|
|
|
|
|
|
|
|
|
Cofactor:
|
|
Heme
|
|
|
|
|
|
Heme
Bound ligand (Het Group name =
HEM)
matches with 95.45% similarity
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
Chembiochem
16:1560-1564
(2015)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
|
|
M.Fischer,
B.K.Shoichet,
J.S.Fraser.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Interrogating fragment libraries by X-ray crystallography is a powerful strategy
for discovering allosteric ligands for protein targets. Cryocooling of crystals
should theoretically increase the fraction of occupied binding sites and
decrease radiation damage. However, it might also perturb protein conformations
that can be accessed at room temperature. Using data from crystals measured
consecutively at room temperature and at cryogenic temperature, we found that
transient binding sites could be abolished at the cryogenic temperatures
employed by standard approaches. Changing the temperature at which the
crystallographic data was collected could provide a deliberate perturbation to
the equilibrium of protein conformations and help to visualize hidden sites with
great potential to allosterically modulate protein function.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Links
