PDBsum entry 4xv5

Oxidoreductase

PDB id: 4xv5

Contents

Protein chain

289 a.a.

Ligands

HEM

BZI ×2

Waters ×253

PDB id:

4xv5

Name:

Oxidoreductase

Title:

Ccp gateless cavity

Structure:

CytochromE C peroxidase, mitochondrial. Chain: a. Fragment: unp residues 71-362. Synonym: ccp. Engineered: yes. Mutation: 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:

1.65Å R-factor: 0.114 R-free: 0.150

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: 26032594 DOI: 10.1002/cbic.201500196

Date:

26-Jan-15 Release date: 25-Feb-15

Protein chain

P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 361 a.a.

Struc: 289 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• 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
• 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

Added reference

DOI no: 10.1002/cbic.201500196

Chembiochem 16:1560-1564 (2015)

PubMed id: 26032594

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.