3WTG | pdb_00003wtg

Crystal structure of Emu (dromaius novaehollandiae) hemoglobin at 2.3 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb3WTG/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Dromaius novaehollandiae
Mutation(s): No

Deposited: 2014-04-11 Released: 2014-07-02
Deposition Author(s): Abubakkar, M.M., Maheshwaran, V., Ponnuswamy, M.N., Saraboji, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.252 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Purification and preliminary structural studies of hemoglobin from high oxygen affinity species Emu (Dromaius novaehollandiae) at neutral pH

Abubakkar, M.M., Saraboji, K., Ponnuswamy, M.N.

To be published.

Macromolecule Content

Total Structure Weight: 66.4 kDa
Atom Count: 4,959
Modeled Residue Count: 568
Deposited Residue Count: 576
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-A	A, C	142	Dromaius novaehollandiae	Mutation(s): 0
UniProt
Find proteins for C6L8R0 (Dromaius novaehollandiae) Explore C6L8R0 Go to UniProtKB: C6L8R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6L8R0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin	B, D	146	Dromaius novaehollandiae	Mutation(s): 0
UniProt
Find proteins for A0A075B5G0 (Dromaius novaehollandiae) Explore A0A075B5G0 Go to UniProtKB: A0A075B5G0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A075B5G0
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 I [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], I [auth C], K [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 I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.252 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.271	α = 90
b = 80.01	β = 90
c = 103.559	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description