5Q4M

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 87)

• PDB DOI: https://doi.org/10.2210/pdb5Q4M/pdb
• Deposition Group: G_1002036 ExploreG_1002036

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-05-25 Released: 2018-08-08 
• Deposition Author(s): Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

PanDDA analysis group deposition

Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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: 39.08 kDa 
• Atom Count: 3,044 
• Modelled Residue Count: 341 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DCLRE1A	A	343	Homo sapiens	Mutation(s): 0  Gene Names: DCLRE1A, KIAA0086, SNM1, SNM1A EC: 3.5.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJP8 (Homo sapiens) Explore Q6PJP8  Go to UniProtKB:  Q6PJP8
PHAROS:  Q6PJP8 GTEx:  ENSG00000198924

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.245 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.247	α = 90
b = 57.35	β = 90
c = 115.308	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references