5HLL

Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO.

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

  • Deposited: 2016-01-15 Released: 2016-03-02 
  • Deposition Author(s): Helliwell, J.R.
  • Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:4g4a


Literature

Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO.

Tanley, S.W.Schreurs, A.M.Kroon-Batenburg, L.M.Helliwell, J.R.

(2016) Acta Crystallogr F Struct Biol Commun 72: 253-254

  • DOI: 10.1107/S2053230X16000856
  • Primary Citation of Related Structures:  
    5HLL

  • PubMed Abstract: 
  • A re-refinement of 4g4a, the room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO is published as an addendum to Tanley et al. [(2012), Acta Cryst. F68, 1300-1306] ...

    A re-refinement of 4g4a, the room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO is published as an addendum to Tanley et al. [(2012), Acta Cryst. F68, 1300-1306]. This example illustrates the benefits of sharing raw diffraction images, as well as structure factors and molecular coordinates, as the diffraction resolution of the study is now much improved at 1.70 Å.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213

    Organizational Affiliation

    School of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester M13 9PL, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], H [auth A], I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NH3
Query on NH3

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A]AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1443α = 90
b = 79.1443β = 90
c = 37.9968γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-15 
  • Released Date: 2016-03-02 
  • Deposition Author(s): Helliwell, J.R.
  • This entry supersedes: 4G4A

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.5: 2020-12-16
    Changes: Advisory, Derived calculations