6R2O | pdb_00006r2o

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

• PDB DOI: https://doi.org/10.2210/pdb6R2O/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2019-03-18 Released: 2020-01-29 
• Deposition Author(s): Oberthuer, D., Yefanov, O., Sarrou, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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

• PubMed: 32005876 
• DOI: https://doi.org/10.1038/s41467-020-14434-6
• Primary Citation 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: 
• CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
DESY, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.
EuXFEL, Sample Environment & Characterization Group, European XFEL Holzkoppel 4, 22869, Schenefeld, Germany.
CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany.
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, 22761, Germany.
Synchrotron Radiation Research, Lund University, Box 118, SE-221 00, Lund, Sweden.
Helmholtz-Zentrum Geesthacht, Institut für Werkstoffforschung, Max-Planck-Straße. 1, 21502, Geesthacht, Germany.
CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. [e-mail].
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. [e-mail].
CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany. [e-mail].
CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. [e-mail].
IBBS, Institut für Biomaterialien und Biomolekulare Systeme, Universität Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.72 kDa 
• Atom Count: 4,797 
• Modeled Residue Count: 572 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P01958 (Equus caballus) Explore P01958  Go to UniProtKB:  P01958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	145	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02062 (Equus caballus) Explore P02062  Go to UniProtKB:  P02062

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	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	L [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1601629

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.5	α = 90
b = 80.8	β = 90
c = 110.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Oberthuer, D., Yefanov, O., Sarrou, I.

Revision History  

• 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