Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.64 kDa 
• Atom Count: 6079 
• Modelled Residue Count: 756 
• Deposited Residue Count: 767 
• Unique protein chains: 3

3S39

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

• PDB DOI: 10.2210/pdb3S39/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Thermus thermophilus HB8
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2011-05-17 Released: 2012-05-23 
• Deposition Author(s): Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.80 Å
• R-Value Free: 0.341 
• R-Value Work: 0.315 
• R-Value Observed: 0.317 

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

• PubMed: 22607023 
• DOI: 10.1021/bi3003988
• Primary Citation of Related Structures:  
  3S33, 3S38, 3S39, 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 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.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	568	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaA, TTHA1135 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79  Go to UniProtKB:  Q5SJ79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B	166	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaB, cbac, ctaC, TTHA1134 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80  Go to UniProtKB:  Q5SJ80

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 2A	C	33	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaD, TTHA1133 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543  Go to UniProtKB:  P82543

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAS	F [auth A]	HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-QIHJKJTBDH
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XE	G [auth A], H [auth A], I [auth A], J [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
CUA	K [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.80 Å
• R-Value Free: 0.341 
• R-Value Work: 0.315 
• R-Value Observed: 0.317 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.61	α = 90
b = 113.61	β = 90
c = 176.55	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-17 
• Released Date: 2012-05-23 
Deposition Author(s): Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D.

Revision History  

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