5E4P | pdb_00005e4p

X-ray Crystal Structure Analysis of Magnetically Oriented Microcrystals of Lysozyme at 1.8 angstrom Resolution

• PDB DOI: https://doi.org/10.2210/pdb5E4P/pdb

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


• Deposited: 2015-10-06 Released: 2016-08-31 
• Deposition Author(s): Tsukui, S., Kimura, F., Garman, E.F., Baba, S., Mizuno, N., Mikami, B., Kimura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure analysis of magnetically oriented microcrystals of lysozyme at 1.8 A resolution

Tsukui, S., Kimura, F., Garman, E.F., Baba, S., Mizuno, N., Mikami, B., Kimura, T.

(2016) J Appl Crystallogr 49: 457-461

• DOI: https://doi.org/10.1107/S1600576716001357

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: 14.33 kDa 
• Atom Count: 1,092 
• Modelled 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.11	α = 90
b = 49.4	β = 90
c = 60.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Tsukui, S., Kimura, F., Garman, E.F., Baba, S., Mizuno, N., Mikami, B., Kimura, T.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary