5IDD

Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.

• PDB DOI: https://doi.org/10.2210/pdb5IDD/pdb
• Entry: 5IDD supersedes: 4OXE

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


• Deposited: 2016-02-24 Released: 2016-05-18 
• Deposition Author(s): Tanley, S.W.M., Helliwell, J.R.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Starting Model: experimental

Re-refinement Note

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

Literature

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)].

Tanley, S.W., Helliwell, J.R.

(2016) Struct Dyn 3: 037101-037101

• PubMed: 27226979 
• DOI: https://doi.org/10.1063/1.4948613
• Primary Citation of Related Structures:  
  5HMV, 5HQ1, 5I5Q, 5IDD

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Organizational Affiliation: 

School of Chemistry, University of Manchester , Manchester M13 9PL, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1,112 
• Modelled Residue Count: 128 
• 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	H [auth A], I [auth A], J [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	L [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NO3	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], M [auth A], N [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
ACT	O [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	G [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.15127/1.266902

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.957	α = 88.76
b = 31.794	β = 71.99
c = 34.055	γ = 68.33

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
APEX 2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Tanley, S.W.M., Helliwell, J.R.
• This entry supersedes: 4OXE

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

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2018-08-08
  Changes: Data collection, Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary