8SF1 | pdb_00008sf1

Carbonic anhydrase II XFEL radiation damage RT

• PDB DOI: https://doi.org/10.2210/pdb8SF1/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-10 Released: 2024-03-13 
• Deposition Author(s): Combs, J.E., Mckenna, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.207 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures.

Hull, J.A., Lee, C., Kim, J.K., Lim, S.W., Park, J., Park, S., Lee, S.J., Park, G., Eom, I., Kim, M., Hyun, H., Combs, J.E., Andring, J.T., Lomelino, C., Kim, C.U., McKenna, R.

(2024) Acta Crystallogr D Struct Biol 80: 194-202

• PubMed: 38411550 
• DOI: https://doi.org/10.1107/S2059798324000482
• Primary Citation Related Structures: 
  8SD1, 8SD6, 8SD7, 8SD8, 8SD9, 8SF1


• PubMed Abstract: 
  

  The combination of X-ray free-electron lasers (XFELs) with serial femtosecond crystallography represents cutting-edge technology in structural biology, allowing the study of enzyme reactions and dynamics in real time through the generation of `molecular movies'. This technology combines short and precise high-energy X-ray exposure to a stream of protein microcrystals. Here, the XFEL structure of carbonic anhydrase II, a ubiquitous enzyme responsible for the interconversion of CO ₂ and bicarbonate, is reported, and is compared with previously reported NMR and synchrotron X-ray and neutron single-crystal structures.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.35 kDa 
• Atom Count: 2,240 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.207 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.92	α = 90
b = 42.01	β = 104.58
c = 73.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Combs, J.E., Mckenna, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release