2RAO | pdb_00002rao

X ray crystal structure of rabbit hemoglobin (oxy form) at 2.0 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb2RAO/pdb

Classification: OXYGEN BINDING
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2007-09-17 Released: 2008-09-09
Deposition Author(s): Sundaresan, S., Packianathan, C., Neelagandan, K., Ponnuswamy, M.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.219 (Depositor), 0.183 (DCC)
R-Value Work:
0.171 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

X-ray crystal structure determination of hemoglobin from rabbit at 2.0 angstrom resloution

Sundaresan, S., Packianathan, C., Neelagandan, K., Ponnuswamy, M.N.

To be published.

Macromolecule Content

Total Structure Weight: 65.61 kDa
Atom Count: 4,833
Modeled Residue Count: 574
Deposited Residue Count: 574
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-1/2	A, C	141	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P01948 (Oryctolagus cuniculus) Explore P01948 Go to UniProtKB: P01948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01948
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta-1/2	B, D	146	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P02057 (Oryctolagus cuniculus) Explore P02057 Go to UniProtKB: P02057
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02057
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth C], K [auth D]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219 (Depositor), 0.183 (DCC)
R-Value Work: 0.171 (Depositor), 0.174 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.608	α = 67.23
b = 54.862	β = 66.35
c = 64.021	γ = 60.68

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-10-14
Changes: Structure summary
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations