5HMJ

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

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

  • 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: 1.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

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: 4xan


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: https://doi.org/10.1107/S2053230X16000777
  • Primary Citation of Related Structures:  
    5HMJ

  • 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 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).


  • 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)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
K [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
T [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS
Query on DMS

Download Ideal Coordinates CCD File 
R [auth A],
S [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
Q [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.58α = 90
b = 78.58β = 90
c = 37.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
EVALdata scaling
EVALdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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: 2016-03-09
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description