4ZGC | pdb_00004zgc

Crystal Structure Analysis of Kelch protein (with disulfide bond) from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb4ZGC/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Plasmodium falciparum
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-04-22 Released: 2015-06-10 
• Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Ravichandran, M., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hui, R., Hutchinson, A., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of kelch protein with disulfide bond from Plasmodium falciparum.

Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Ravichandran, M., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hutchinson, A., Lin, Y.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.47 kDa 
• Atom Count: 5,898 
• Modeled Residue Count: 745 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch protein	A, B	389	Plasmodium falciparum	Mutation(s): 0  Gene Names: PF13_0238
UniProt
Find proteins for Q8IDQ2 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDQ2  Go to UniProtKB:  Q8IDQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.942	α = 90
b = 117.634	β = 113.77
c = 74.508	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Ravichandran, M., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hui, R., Hutchinson, A., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Database references, Structure summary
• Version 1.2: 2017-09-27
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary