4XDI

Structure of Chlamydomonas reinhardtii THB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine-lysine heme ligation.

Rice, S.L.Boucher, L.E.Schlessman, J.L.Preimesberger, M.R.Bosch, J.Lecomte, J.T.

(2015) Acta Crystallogr.,Sect.F 71: 718-725

  • DOI: 10.1107/S2053230X15006949

  • PubMed Abstract: 
  • THB1 is one of several group 1 truncated hemoglobins (TrHb1s) encoded in the genome of the unicellular green alga Chlamydomonas reinhardtii. THB1 expression is under the control of NIT2, the master regulator of nitrate assimilation, which also contro ...

    THB1 is one of several group 1 truncated hemoglobins (TrHb1s) encoded in the genome of the unicellular green alga Chlamydomonas reinhardtii. THB1 expression is under the control of NIT2, the master regulator of nitrate assimilation, which also controls the expression of the only nitrate reductase in the cell, NIT1. In vitro and physiological evidence suggests that THB1 converts the nitric oxide generated by NIT1 into nitrate. To aid in the elucidation of the function and mechanism of THB1, the structure of the protein was solved in the ferric state. THB1 resembles other TrHb1s, but also exhibits distinct features associated with the coordination of the heme iron by a histidine (proximal) and a lysine (distal). The new structure illustrates the versatility of the TrHb1 fold, suggests factors that stabilize the axial ligation of a lysine, and highlights the difficulty of predicting the identity of the distal ligand, if any, in this group of proteins.


    Organizational Affiliation

    Chemistry Department, US Naval Academy, 572 Holloway Road, Annapolis, MD 21402, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.,Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chlamydomonas reinhardtii THB1
A, B
135Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: THB1
Find proteins for A8JAR4 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JAR4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 144.513α = 90.00
b = 144.513β = 90.00
c = 79.913γ = 120.00
Software Package:
Software NamePurpose
SHELXDEphasing
SHELXphasing
XSCALEdata scaling
XDSdata scaling
PHENIXrefinement
CrysalisProdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1330488

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Data collection
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description