Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

 2DC3

Crystal structure of human cytoglobin at 1.68 angstroms resolution

• PDB DOI: 10.2210/pdb2DC3/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-21 Released: 2006-05-23 
• Deposition Author(s): Makino, M., Sugimoto, H., Sawai, H., Kawada, N., Yoshizato, K., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.181 
• R-Value Work: 0.140 
• R-Value Observed: 0.142 

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

• PubMed: 16699195 
• DOI: 10.1107/S0907444906013813
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoglobin	A, B	193	Homo sapiens	Mutation(s): 0  Gene Names: CYGB, STAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWM9 (Homo sapiens) Explore Q8WWM9  Go to UniProtKB:  Q8WWM9
PHAROS:  Q8WWM9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.181 
• R-Value Work: 0.140 
• R-Value Observed: 0.142 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.53	α = 90
b = 52.76	β = 87.75
c = 83.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Makino, M., Sugimoto, H., Sawai, H., Kawada, N., Yoshizato, K., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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