3BCQ | pdb_00003bcq

Crystal structure of oxy-hemoglobin from Brycon cephalus

• PDB DOI: https://doi.org/10.2210/pdb3BCQ/pdb

• Classification: TRANSPORT PROTEIN/OXYGEN BINDING
• Organism(s): Brycon cephalus
• Mutation(s): No 


• Deposited: 2007-11-13 Released: 2008-10-07 
• Deposition Author(s): Poy, C.D., Leopoldino, A.M., Rahal, P., de Azevedo, W.F., Rodriguez, G.O.B., Murakami, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.279 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of oxy-hemoglobin from Brycon cephalus

Poy, C.D., Leopoldino, A.M., Rahal, P., de Azevedo, W.F., Rodriguez, G.O.B., Murakami, M.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 66.26 kDa 
• Atom Count: 4,772 
• Modeled Residue Count: 576 
• Deposited Residue Count: 576 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-chain hemoglobin	A, C	142	Brycon cephalus	Mutation(s): 0
UniProt
Find proteins for A1YZP4 (Brycon cephalus) Explore A1YZP4  Go to UniProtKB:  A1YZP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-chain hemoglobin	B, D	146	Brycon cephalus	Mutation(s): 0
UniProt
Find proteins for D0VWS2 (Brycon cephalus) Explore D0VWS2  Go to UniProtKB:  D0VWS2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OXY	F [auth A], H [auth B], J [auth C], L [auth D]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.279 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.366	α = 90
b = 54.039	β = 113.89
c = 101.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Poy, C.D., Leopoldino, A.M., Rahal, P., de Azevedo, W.F., Rodriguez, G.O.B., Murakami, M.T.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description