9EWK | pdb_00009ewk

Solvent organization in ultrahigh-resolution protein crystal structure at room temperature

• PDB DOI: https://doi.org/10.2210/pdb9EWK/pdb

• Classification: PLANT PROTEIN
• Organism(s): Crambe hispanica subsp. abyssinica
• Mutation(s): Yes 


• Deposited: 2024-04-04 Released: 2024-09-04 
• Deposition Author(s): Chen, J.C.-H., Gilski, M., Chang, C., Borek, D., Rosenbaum, G., Lavens, A., Otwinowski, Z., Kubicki, M., Dauter, Z., Jaskolski, M., Joachimiak, A.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.70 Å
• R-Value Work: 
  0.076 (Depositor), 0.068 (DCC) 

Starting Model: experimental

Literature

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature.

Chen, J.C.H., Gilski, M., Chang, C., Borek, D., Rosenbaum, G., Lavens, A., Otwinowski, Z., Kubicki, M., Dauter, Z., Jaskolski, M., Joachimiak, A.

(2024) IUCrJ 11: 649-663

• PubMed: 39190507 
• DOI: https://doi.org/10.1107/S2052252524007784
• Primary Citation Related Structures: 
  9EWK


• PubMed Abstract: 
  

  Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL. Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

---

Organizational Affiliation: 
• Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań Poland.
Department of Biophysics and Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX USA.
Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Poznań, Poland.
Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 4.82 kDa 
• Atom Count: 546 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crambin	A	46	Crambe hispanica subsp. abyssinica	Mutation(s): 2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica) Explore P01542  Go to UniProtKB:  P01542

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	B [auth A], C [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.70 Å
• R-Value Work:  0.076 (Depositor), 0.068 (DCC) 

Diffraction Data: https://doi.org/10.18150/1RI4XW

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.725	α = 90
b = 18.767	β = 90.55
c = 41.059	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Chen, J.C.-H., Gilski, M., Chang, C., Borek, D., Rosenbaum, G., Lavens, A., Otwinowski, Z., Kubicki, M., Dauter, Z., Jaskolski, M., Joachimiak, A.

---

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM145365

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-09-11
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Structure summary