3K2R | pdb_00003k2r

Crystal Structure of Spin Labeled T4 Lysozyme Mutant K65V1/R76V1

• PDB DOI: https://doi.org/10.2210/pdb3K2R/pdb

• Classification: HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-30 Released: 2010-10-13 
• Deposition Author(s): Toledo Warshaviak, D., Cascio, D., Khramtsov, V.V., Hubbell, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Spin Labeled T4 Lysozyme Mutant K65V1/R76V1

Toledo Warshaviak, D., Cascio, D., Khramtsov, V.V., Hubbell, W.L.

To be published.

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: 19.4 kDa 
• Atom Count: 1,492 
• Modeled Residue Count: 162 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	164	Tequatrovirus T4	Mutation(s): 4  Gene Names: E, Lysozyme EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V1A	B [auth A], D [auth A]	S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate C8 H15 N2 O3 S2 GGUBULNJTWFONN-UHFFFAOYSA-N
HEZ	C [auth A], E [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
K	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.547	α = 90
b = 59.547	β = 90
c = 95.28	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Toledo Warshaviak, D., Cascio, D., Khramtsov, V.V., Hubbell, W.L.

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Other
• Version 1.3: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.4: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary