5HMJ

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

• PDB DOI: https://doi.org/10.2210/pdb5HMJ/pdb
• Entry: 5HMJ supersedes: 4XAN

• 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

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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 

Starting Model: experimental

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

• PubMed: 26919531 
• 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).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.88 kDa 
• Atom Count: 1,150 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	K [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
BR	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	R [auth A], S [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	Q [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.215 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.15127/1.266906

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.58	α = 90
b = 78.58	β = 90
c = 37.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
EVAL	data scaling
EVAL	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History  

• 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
• Version 1.6: 2024-10-16
  Changes: Structure summary