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

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.,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
PHASERphasing
EVALdata scaling
PHENIXrefinement
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