4BAP | pdb_00004bap

Hen egg-white lysozyme structure in complex with the europium tris- hydroxyethylcholinetriazoledipicolinate complex at 1.21 A resolution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 
    0.178 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4BAP

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination.

Talon, R., Nauton, L., Canet, J.-L., Kahn, R., Girard, E., Gautier, A.

(2012) Chem Commun (Camb) 48: 11886

  • DOI: https://doi.org/10.1039/c2cc36982f
  • Primary Citation Related Structures: 
    4BAD, 4BAF, 4BAL, 4BAP, 4BAR

  • PubMed Abstract: 

    New trisdipicolinic acid-lanthanide complexes are reported as phasing agents for X-ray crystallography of proteins. It is demonstrated that CuAAC modifications allow protein co-crystallization with low concentration of lanthanide complexes leading to an accurate structure determination.

    • Organizational Affiliation: 
    • CEA, DSV, Institut de Biologie Structurale (IBS), 41 rue Jules Horowitz, Grenoble F-38027, France.

Macromolecule Content 

  • Total Structure Weight: 15.88 kDa 
  • Atom Count: 1,352 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LYSOZYME C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DCJ

Query on DCJ


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]		N-((1-(2,6-DICARBOXYPYRIDIN-4-YL)-1H-1,2,3-TRIAZOL-4-YL)METHYL)-2-HYDROXY-N,N-DIMETHYLETHANAMINIUM
C14 H18 N5 O5
AQWWXXIJXFAABJ-UHFFFAOYSA-O
EU3

Query on EU3


Download:Ideal Coordinates CCD File
P [auth A]EUROPIUM (III) ION
Eu
LNBHUCHAFZUEGJ-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL


Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA


Download:Ideal Coordinates CCD File
N [auth A],
O [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free:  0.178 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.509α = 90
b = 77.509β = 90
c = 38.482γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary