3QM9

Blackfin tuna azido-myoglobin, atomic resolution

PDB DOI: https://doi.org/10.2210/pdb3QM9/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Thunnus atlanticus
Mutation(s): No

Deposited: 2011-02-03 Released: 2012-02-08
Deposition Author(s): de Serrano, V.S., Rodriguez, M.M., Schreiter, E.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.91 Å
R-Value Free: 0.133
R-Value Work: 0.120
R-Value Observed: 0.121

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High Resolution Structures of Blackfin Tuna Myoglobin

de Serrano, V.S., Rodriguez, M.M., Schreiter, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 16.51 kDa
Atom Count: 1,665
Modelled Residue Count: 146
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	146	Thunnus atlanticus	Mutation(s): 0
UniProt
Find proteins for H3JQV6 (Thunnus atlanticus) Explore H3JQV6 Go to UniProtKB: H3JQV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H3JQV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.91 Å
R-Value Free: 0.133
R-Value Work: 0.120
R-Value Observed: 0.121
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.008	α = 90
b = 51.894	β = 103.95
c = 38.644	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

de Serrano, V.S.

Rodriguez, M.M.

Schreiter, E.R.

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3QM9

Blackfin tuna azido-myoglobin, atomic resolution

High Resolution Structures of Blackfin Tuna Myoglobin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)