8PUQ | pdb_00008puq

MetHemoglobin structure from serial synchrotron crystallography with fixed target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.125 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8PUQ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes.

Bjelcic, M.Sigfridsson Clauss, K.G.V.Aurelius, O.Milas, M.Nan, J.Ursby, T.

(2023) Acta Crystallogr D Struct Biol 79: 1018-1025

  • DOI: https://doi.org/10.1107/S205979832300880X
  • Primary Citation Related Structures: 
    8PUQ, 8PUR

  • PubMed Abstract: 

    In recent years, the emergence of serial crystallography, initially pioneered at X-ray free-electron lasers (XFELs), has sparked a growing interest in collecting macromolecular crystallographic data at room temperature. Various fixed-target serial crystallography techniques have been developed, ranging from commercially available chips to in-house designs implemented at different synchrotron facilities. Nevertheless, there is currently no commercially available chip (known to the authors) specifically designed for the direct handling of oxygen-sensitive samples. This study presents a methodology employing silicon nitride chips arranged in a `sandwich' configuration, enabling reliable room-temperature data collection from oxygen-sensitive samples. The method involves the utilization of a custom-made 3D-printed assembling tool and a MX sample holder. To validate the effectiveness of the proposed method, deoxyhemoglobin and methemoglobin samples were investigated using the BioMAX X-ray macromolecular crystallography beamline, the Balder X-ray absorption spectroscopy beamline and UV-Vis absorption spectroscopy.


  • Organizational Affiliation
    • MAX IV Laboratory, Lund University, PO Box 118, SE-221 00 Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 32.25 kDa 
  • Atom Count: 2,378 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 286 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha140Equus caballusMutation(s): 0 
UniProt
Find proteins for P01958 (Equus caballus)
Explore P01958 
Go to UniProtKB:  P01958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01958
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta146Equus caballusMutation(s): 0 
UniProt
Find proteins for P02062 (Equus caballus)
Explore P02062 
Go to UniProtKB:  P02062
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02062
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.125 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.53α = 90
b = 63.08β = 111.02
c = 54.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Database references