2DC3 | pdb_00002dc3

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 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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This is version 1.4 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 D Biol Crystallogr 62: 671-677

  • DOI: https://doi.org/10.1107/S0907444906013813
  • Primary Citation Related Structures: 
    2DC3

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 44.72 kDa 
  • Atom Count: 3,126 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytoglobin
A, B
193Homo sapiensMutation(s): 0 
Gene Names: CYGB
EC: 1.11.1 (UniProt), 1.14.12 (UniProt), 1.15.1.1 (UniProt), 1.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWM9 (Homo sapiens)
Explore Q8WWM9 
Go to UniProtKB:  Q8WWM9
PHAROS:  Q8WWM9
GTEx:  ENSG00000161544 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WWM9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.181 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.53α = 90
b = 52.76β = 87.75
c = 83.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary