2DC3

Crystal structure of human cytoglobin at 1.68 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode.

Makino, M.Sugimoto, H.Sawai, H.Kawada, N.Yoshizato, K.Shiro, Y.

(2006) Acta Crystallogr.,Sect.D 62: 671-677

  • DOI: 10.1107/S0907444906013813

  • PubMed Abstract: 
  • Cytoglobin (Cgb) is a recently discovered member of the vertebrate haem-containing globin family. The structure of a new crystal form of wild-type human Cgb (space group C2) was determined at a resolution of 1.68 Angstrom. The results show the presen ...

    Cytoglobin (Cgb) is a recently discovered member of the vertebrate haem-containing globin family. The structure of a new crystal form of wild-type human Cgb (space group C2) was determined at a resolution of 1.68 Angstrom. The results show the presence of an additional helix in the N-terminal residues (4-20) prior to the A helix and an ordered loop structure in the C-terminal region (168-188), while these extended peptides were invisible owing to disorder in the previously reported structures using a P3(2)21 crystal at a resolution of 2.4 Angstrom. A detailed comparison of the two crystal structures shows differences in the conformation of the residues (i.e. Arg84) in the haem environment owing to a different dimeric arrangement.


    Organizational Affiliation

    Biometal Science Laboratory, Harima Institute, RIKEN SPring-8 Center, Harima Institute, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytoglobin
A, B
193Homo sapiensGene Names: CYGB (STAP)
Find proteins for Q8WWM9 (Homo sapiens)
Go to Gene View: CYGB
Go to UniProtKB:  Q8WWM9
Small Molecules
Ligands 2 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
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.530α = 90.00
b = 52.760β = 87.75
c = 83.440γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance