3WU7 | pdb_00003wu7

Spatiotemporal development of soaked protein crystal; derivative 250 sec

• PDB DOI: https://doi.org/10.2210/pdb3WU7/pdb

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


• Deposited: 2014-04-23 Released: 2014-07-30 
• Deposition Author(s): Mizutani, R., Saiga, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Spatiotemporal development of soaked protein crystal

Mizutani, R., Shimizu, Y., Saiga, R., Ueno, G., Nakamura, Y., Takeuchi, A., Uesugi, K., Suzuki, Y.

(2014) Sci Rep 4: 5731-5731

• PubMed: 25043871 
• DOI: https://doi.org/10.1038/srep05731
• Primary Citation Related Structures: 
  3WPJ, 3WPK, 3WPL, 3WU7, 3WU8, 3WU9, 3WUA


• PubMed Abstract: 
  

  Crystal soaking is widely performed in biological crystallography. This paper reports time-resolved X-ray crystallographic and microtomographic analyses of tetragonal crystals of chicken egg-white lysozyme soaked in mother liquor containing potassium hexachloroplatinate. The microtomographic analysis showed that X-ray attenuation spread from the superficial layer of the crystal and then to the crystal core. The crystallographic analyses indicated that platinum sites can be classified into two groups from the temporal development of the electron densities. A soaking process consisting of binding-rate-driven and equilibrium-driven layers is proposed to describe these results. This study suggests that the composition of chemical and structural species resulting from the soaking process varies depending on the position in the crystal.

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Organizational Affiliation: 
• Department of Applied Biochemistry, School of Engineering, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan.
RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan.
Rigaku Corporation, 14-8, Akaoji-cho, Takatsuki-Shi, Osaka 569-1146, Japan.
Research and Utilization Division, JASRI/SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.72 kDa 
• Atom Count: 1,071 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT4	B [auth A], C [auth A]	PLATINUM (IV) ION Pt NDBYXKQCPYUOMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.174	α = 90
b = 79.174	β = 90
c = 37.902	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Mizutani, R., Saiga, R.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary