1RTX

Crystal Structure of Synechocystis Hemoglobin with a Covalent Heme Linkage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of synechocystis hemoglobin with a covalent heme linkage.

Hoy, J.A.Kundu, S.Trent, J.T.Ramaswamy, S.Hargrove, M.S.

(2004) J.Biol.Chem. 279: 16535-16542

  • DOI: 10.1074/jbc.M313707200

  • PubMed Abstract: 
  • The x-ray crystal structure of Synechocystis hemoglobin has been solved to a resolution of 1.8 A. The conformation of this structure is surprisingly different from that of the previously reported solution structure, probably due in part to a covalent ...

    The x-ray crystal structure of Synechocystis hemoglobin has been solved to a resolution of 1.8 A. The conformation of this structure is surprisingly different from that of the previously reported solution structure, probably due in part to a covalent linkage between the heme 2-vinyl and His117 that is present in the crystal structure but not in the structure solved by NMR. Synechocystis hemoglobin is a hexacoordinate hemoglobin in which the heme iron is coordinated by both the proximal and distal histidines. It is also a member of the "truncated hemoglobin" family that is much shorter in primary structure than vertebrate and plant hemoglobins. In contrast to other truncated hemoglobins, the crystal structure of Synechocystis hemoglobin displays no "ligand tunnel" and shows that several important amino acid side chains extrude into the solvent instead of residing inside the heme pocket. The stereochemistry of hexacoordination is compared with other hexacoordinate hemoglobins and cytochromes in an effort to illuminate factors contributing to ligand affinity in hexacoordinate hemoglobins.


    Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyanoglobin
A
123Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: glbN
Find proteins for P73925 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P73925
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
CD
Query on CD

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Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.500α = 90.00
b = 46.000β = 90.00
c = 61.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SOLVEphasing
RESOLVEphasing
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance