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.

• PDB DOI: https://doi.org/10.2210/pdb5HLL/pdb
• Entry: 5HLL supersedes: 4G4A

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


• Deposited: 2016-01-15 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: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4g4a

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 F Struct Biol Commun 72: 253-254

• PubMed: 26948967 
• DOI: https://doi.org/10.1107/S2053230X16000856
• Primary Citation of Related Structures:  
  5HLL


• 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, 1300-1306]. 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.

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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: 15.02 kDa 
• Atom Count: 1,077 
• 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	F [auth A], G [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	C [auth A], D [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH3	J [auth A], K [auth A], L [auth A]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.15127/1.215887

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1443	α = 90
b = 79.1443	β = 90
c = 37.9968	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Helliwell, J.R.
• This entry supersedes: 4G4A

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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: 2016-04-06
  Changes: Database references
• Version 1.2: 2016-07-27
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2018-08-08
  Changes: Data collection, Database references
• Version 1.5: 2020-12-16
  Changes: Advisory, Derived calculations
• Version 1.6: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-11-06
  Changes: Structure summary