4EPD

Initial Urease Structure for Radiation Damage Experiment at 300 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Spatial distribution of radiation damage to crystalline proteins at 25-300 K.

Warkentin, M.Badeau, R.Hopkins, J.B.Thorne, R.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1108-1117

  • DOI: 10.1107/S0907444912021361
  • Primary Citation of Related Structures:  
    4EK0, 4EKA, 4EKB, 4EKH, 4EKO, 4EKT, 4EL2, 4EL3, 4EL7, 4ELA, 4EP8, 4EPB, 4EPD, 4EPE

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Physics Department, Cornell University, Ithaca, NY 14853, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit alphaA [auth C]566Klebsiella aerogenesMutation(s): 0 
Gene Names: ureC
EC: 3.5.1.5
UniProt
Find proteins for P18314 (Klebsiella aerogenes)
Explore P18314 
Go to UniProtKB:  P18314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18314
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit betaB101Klebsiella aerogenesMutation(s): 0 
Gene Names: ureB
EC: 3.5.1.5
UniProt
Find proteins for P18315 (Klebsiella aerogenes)
Explore P18315 
Go to UniProtKB:  P18315
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18315
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Urease subunit gammaC [auth A]100Klebsiella aerogenesMutation(s): 0 
Gene Names: ureA
EC: 3.5.1.5
UniProt
Find proteins for P18316 (Klebsiella aerogenes)
Explore P18316 
Go to UniProtKB:  P18316
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18316
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth C],
E [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A [auth C]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.765α = 90
b = 170.765β = 90
c = 170.765γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references