4XDI

Structure of Chlamydomonas reinhardtii THB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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This is version 1.5 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 F Struct Biol Commun 71: 718-725

  • DOI: https://doi.org/10.1107/S2053230X15006949
  • Primary Citation of Related Structures:  
    4XDI

  • 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 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

    T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlamydomonas reinhardtii THB1
A, B
135Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: THB1CHLREDRAFT_81856
UniProt
Find proteins for A8JAR4 (Chlamydomonas reinhardtii)
Explore A8JAR4 
Go to UniProtKB:  A8JAR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8JAR4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.513α = 90
b = 144.513β = 90
c = 79.913γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
SHELXphasing
SHELXDEphasing
CrysalisProdata scaling
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Data collection
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references