5HMJ

Re-refinement of 4xan: hen lysozyme with carboplatin in sodium bromide solution

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

  • Deposited: 2016-01-16 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: 1.2999 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

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

  • 4XAN - determined by Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Levy, C., Schreurs, A.M.M., Helliwell, J.R.  

Literature

Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution.

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

(2016) Acta Crystallogr F Struct Biol Commun 72: 251-252

  • DOI: 10.1107/S2053230X16000777

  • PubMed Abstract: 
  • A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135-1142]. This follows a previous re-refinement and ...

    A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135-1142]. This follows a previous re-refinement and PDB deposition (4yem) by Shabalin et al. [(2015), Acta Cryst. D71, 1965-1979]. The critical evaluation of the original PDB deposition (4xan), and the subsequent critical examination of the re-refined structure (4yem), has led to an improved model (PDB code 5hmj).


    Related Citations: 
    • Structural dynamics of cisplatin binding to histidine in a protein.
      Tanley, S.W.,Helliwell, J.R.
      (2014) Struct Dyn 1: 034701


    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 gallusMutation(s): 0 
Gene 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

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

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2999 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.580α = 90.00
b = 78.580β = 90.00
c = 37.290γ = 90.00
Software Package:
Software NamePurpose
EVALdata scaling
PHENIXrefinement
PHASERphasing
EVALdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-16 
  • Released Date: 2016-03-02 
  • Deposition Author(s): Helliwell, J.R.
  • This entry supersedes: 4XAN

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

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references
  • Version 1.4: 2018-08-01
    Type: Data collection, Database references