3L2X | pdb_00003l2x

Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX

• PDB DOI: https://doi.org/10.2210/pdb3L2X/pdb

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


• Deposited: 2009-12-15 Released: 2011-01-05 
• Deposition Author(s): Fleissner, M.R., Cascio, D., Hubbell, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX

Fleissner, M.R., Cascio, D., Kalai, T., Hideg, K., 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: 19.15 kDa 
• Atom Count: 1,508 
• Modeled Residue Count: 164 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RXR	B [auth A]	[2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-yl]oxidanyl radical C10 H18 N O S2 PZEXYXPQVHSRCF-UHFFFAOYSA-N
HED	F [auth A]	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
BME	G [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
AZI	C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.113	α = 90
b = 60.113	β = 90
c = 96.655	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Fleissner, M.R., Cascio, D., Hubbell, W.L.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description