4EPD image
Deposition Date 2012-04-17
Release Date 2012-08-29
Last Version Date 2025-03-26
Entry Detail
PDB ID:
4EPD
Keywords:
Title:
Initial Urease Structure for Radiation Damage Experiment at 300 K
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.16
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
I 21 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Urease subunit gamma
Gene (Uniprot):ureA
Chain IDs:C (auth: A)
Chain Length:100
Number of Molecules:1
Biological Source:Enterobacter aerogenes
Polymer Type:polypeptide(L)
Molecule:Urease subunit beta
Gene (Uniprot):ureB
Chain IDs:B
Chain Length:101
Number of Molecules:1
Biological Source:Enterobacter aerogenes
Polymer Type:polypeptide(L)
Molecule:Urease subunit alpha
Gene (Uniprot):ureC
Chain IDs:A (auth: C)
Chain Length:566
Number of Molecules:1
Biological Source:Enterobacter aerogenes
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX A LYS LYSINE NZ-CARBOXYLIC ACID
Ligand Molecules
Primary Citation
Spatial distribution of radiation damage to crystalline proteins at 25-300 K.
Acta Crystallogr.,Sect.D 68 1108 1117 (2012)
PMID: 22948911 DOI: 10.1107/S0907444912021361

Abstact

The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.

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Primary Citation of related structures