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

  • 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: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

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

  • 4G4A - determined by Tanley, S.W.M., Schreurs, A.M.M., Kroon-Batenburg, L.M.J., Helliwell, J.R.  

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.,Sect.F 72: 253-254

  • DOI: 10.1107/S2053230X16000856

  • 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- ...

    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: 
    • 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.,Sect.D 66: 213
    • 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.,Sect.D 68: 352


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PT
Query on PT

Download SDF File 
Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NH3
Query on NH3

Download SDF File 
Download CCD File 
A
AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.144α = 90.00
b = 79.144β = 90.00
c = 37.997γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

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

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

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection