4LT1 | pdb_00004lt1

HEWL co-crystallised with Carboplatin in non-NaCl conditions: crystal 1 processed using the XDS software package

• PDB DOI: https://doi.org/10.2210/pdb4LT1/pdb

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


• Deposited: 2013-07-23 Released: 2014-07-23 
• Deposition Author(s): Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Schreurs, A.M.M., Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Carboplatin binding to a model protein in non-NaCl conditions to eliminate partial conversion to cisplatin, and the use of different criteria to choose the resolution limit

Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Schreurs, A.M.M., Helliwell, J.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.37 kDa 
• Atom Count: 1,083 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QPT	D [auth A]	carboplatin C6 H12 N2 O4 Pt BHKICZDKIIDMNR-UHFFFAOYSA-L
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS	B [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.82	α = 90
b = 76.82	β = 90
c = 36.47	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Schreurs, A.M.M., Helliwell, J.R.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary