9T6V | pdb_00009t6v

Low-dose (32.5 kGy) structure of horse-heart myoglobin at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.147 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Coupled on-line in crystallo UV-Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature.

Caramello, N.Rose, S.L.Mathieu, E.Petit, L.Tews, I.Engilberge, S.Royant, A.

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326000690
  • Primary Citation of Related Structures:  
    9T6O, 9T6P, 9T6Q, 9T6U, 9T6V, 9T6W, 9T6X, 9T6Y

  • PubMed Abstract: 

    Specific radiation damage (SRD) to proteins is a pertinent issue discovered during the development of cryo-crystallography at synchrotrons, often affecting the macromolecular active site and thus complicating the understanding of mechanistic insights from structural analysis. For proteins with a spectroscopic signature in the visible light spectrum, in crystallo UV-Vis absorption spectroscopy has regularly been used to estimate the dose scale of specific damage build-up and to develop diffraction data-collection strategies to mitigate its effects. Using a coupled spectroscopic and crystallographic approach, here we show that for two metal-containing proteins the structural response to X-ray-induced reduction of metals in their active site is markedly different at room temperature than at cryogenic temperature. This suggests that the use of controlled specific radiation damage to mimic and study a physiological redox transition in a metal-containing protein by X-ray crystallography should preferably be performed at room temperature rather than at cryogenic temperature.


  • Organizational Affiliation
    • Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38044 Grenoble, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Equus caballusMutation(s): 0 
Gene Names: MB
EC: 1.7 (PDB Primary Data), 1.11.1 (PDB Primary Data)
UniProt
Find proteins for P68082 (Equus caballus)
Explore P68082 
Go to UniProtKB:  P68082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68082
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.147 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.106α = 90
b = 35.825β = 90
c = 125.324γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INSB-05-02
Agence Nationale de la Recherche (ANR)FranceANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release