6R2O

Hemoglobin structure from serial crystallography with a 3D-printed nozzle.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ultracompact 3D microfluidics for time-resolved structural biology.

Knoska, J.Adriano, L.Awel, S.Beyerlein, K.R.Yefanov, O.Oberthuer, D.Pena Murillo, G.E.Roth, N.Sarrou, I.Villanueva-Perez, P.Wiedorn, M.O.Wilde, F.Bajt, S.Chapman, H.N.Heymann, M.

(2020) Nat Commun 11: 657-657

  • DOI: https://doi.org/10.1038/s41467-020-14434-6
  • Primary Citation of Related Structures:  
    6R2O

  • PubMed Abstract: 

    To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s -1 , which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.


  • Organizational Affiliation

    Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. henry.chapman@cfel.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
141Equus 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
145Equus 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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.5α = 90
b = 80.8β = 90
c = 110.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-01-24
    Changes: Refinement description