8CW7 | pdb_00008cw7

200us Temperature-Jump (Dark2) XFEL structure of Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb8CW7/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2022-05-18 Released: 2022-06-22 
• Deposition Author(s): Wolff, A.M., Thompson, M.C., Fraser, J.S., Nango, E.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.

Wolff, A.M., Nango, E., Young, I.D., Brewster, A.S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B.A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J.M., Im, D., O'Riordan, L.J., Tanaka, T., Tanaka, R., Sierra, R.G., Yumoto, F., Tono, K., Iwata, S., Sauter, N.K., Fraser, J.S., Thompson, M.C.

(2023) Nat Chem 15: 1549-1558

• PubMed: 37723259 
• DOI: https://doi.org/10.1038/s41557-023-01329-4
• Primary Citation Related Structures: 
  8CVU, 8CVV, 8CVW, 8CW0, 8CW1, 8CW3, 8CW5, 8CW6, 8CW7, 8CW8, 8CWB, 8CWC, 8CWD, 8CWE, 8CWF, 8CWG, 8CWH


• PubMed Abstract: 
  

  Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA.
RIKEN SPring-8 Center, Sayo-gun, Japan. [e-mail].
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Japan. [e-mail].
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
RIKEN SPring-8 Center, Sayo-gun, Japan.
Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan.
Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA.
Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, Izunokuni-shi, Japan.
SLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA, USA.
Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Japan.
Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Japan.
Ginward Japan K.K., Tokyo, Japan.
Japan Synchrotron Radiation Research Institute, Hyogo, Japan.
Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.65 kDa 
• Atom Count: 1,203 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1873469

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.457	α = 90
b = 79.457	β = 90
c = 38.187	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
cxi.merge	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Wolff, A.M., Thompson, M.C., Fraser, J.S., Nango, E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Refinement description
• Version 1.4: 2023-11-15
  Changes: Database references
• Version 1.5: 2024-10-23
  Changes: Structure summary