3S39

Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.8 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.315 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.

Luna, V.M.Fee, J.A.Deniz, A.A.Stout, C.D.

(2012) Biochemistry 51: 4669-4676

  • DOI: 10.1021/bi3003988
  • Primary Citation of Related Structures:  3S33, 3S38, 3S3A, 3S3B, 3S3C, 3S3D

  • PubMed Abstract: 
  • We use a form of "freeze-trap, kinetic crystallography" to explore the migration of Xe atoms away from the dinuclear heme a(3)/Cu(B) center in Thermus thermophilus cytochrome ba(3) oxidase. This enzyme is a member of the heme-copper oxidase superfami ...

    We use a form of "freeze-trap, kinetic crystallography" to explore the migration of Xe atoms away from the dinuclear heme a(3)/Cu(B) center in Thermus thermophilus cytochrome ba(3) oxidase. This enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O(2) diffusion channel in cytochrome ba(3) oxidase that is continuous, Y-shaped, 18-20 Å in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a(3)-Cu(B) center in the active site. To understand movement of gas molecules within the O(2) channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 s while undergoing outgassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 → Xe5 → Xe3 → Xe4 sites, suggesting that ingress of O(2) is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. vmitchluna@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A
568Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaA
EC: 1.9.3.1
Find proteins for Q5SJ79 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ79
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B
166Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaB (ctaC)
EC: 1.9.3.1
Find proteins for Q5SJ80 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ80
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide 2A
C
33Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: cbaD
EC: 1.9.3.1
Find proteins for P82543 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P82543
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAS
Query on HAS

Download SDF File 
Download CCD File 
A
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
 Ligand Interaction
CUA
Query on CUA

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Download CCD File 
B
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
XE
Query on XE

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Download CCD File 
A
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.8 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.315 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.610α = 90.00
b = 113.610β = 90.00
c = 176.550γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-05-30
    Type: Database references
  • Version 1.2: 2012-09-12
    Type: Database references