1A3N | pdb_00001a3n

DEOXY HUMAN HEMOGLOBIN

• PDB DOI: https://doi.org/10.2210/pdb1A3N/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1998-01-22 Released: 1998-04-29 
• Deposition Author(s): Tame, J., Vallone, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.160 (DCC) 

Literature

The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K.

Tame, J.R., Vallone, B.

(2000) Acta Crystallogr D Biol Crystallogr 56: 805-811

• PubMed: 10930827 
• DOI: https://doi.org/10.1107/s0907444900006387
• Primary Citation of Related Structures:  
  1A3N, 1A3O


• PubMed Abstract: 
  

  The structures of deoxy human haemoglobin and an artificial mutant (Tyralpha42-->His) have been solved at 120 K. While overall agreement between these structures and others in the PDB is very good, certain side chains are found to be shifted, absent from the electron-density map or in different rotamers. Non-crystallographic symmetry (NCS) is very well obeyed in the native protein, but not around the site of the changed residue in the mutant. NCS is also not obeyed by the water molecule invariably found in the alpha-chain haem pocket in room-temperature crystal structures of haemoglobin. At 120 K, this water molecule disappears from one alpha chain in the asymmetric unit but not the other.

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Organizational Affiliation: 

Protonic Nanomachine Project, ERATO, 3-4 Hikaridai, Seika, Kyoto 619-0237, Japan. [e-mail].

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: 64.55 kDa 
• Atom Count: 4,997 
• Modeled Residue Count: 572 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN (ALPHA CHAIN)	A, C	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN (BETA CHAIN)	B, D	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.160 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.65	α = 90
b = 82.43	β = 99.61
c = 53.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-04-29 
Deposition Author(s): Tame, J., Vallone, B.

Revision History  

• Version 1.0: 1998-04-29
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other