4YY8 | pdb_00004yy8

Crystal Structure Analysis of Kelch protein from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb4YY8/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Plasmodium falciparum
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-03-23 Released: 2015-04-01 
• 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: 1.81 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Kelch protein 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., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hui, R., Hutchinson, A., Lin, Y.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 89.02 kDa 
• Atom Count: 6,510 
• Modeled Residue Count: 750 
• 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 A0A077LQB4 (Plasmodium falciparum) Explore A0A077LQB4  Go to UniProtKB:  A0A077LQB4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	IA [auth B], JA [auth B], KA [auth B], LA [auth B], U [auth A], V [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
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], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.189	α = 90
b = 117.02	β = 113.88
c = 74.566	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
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: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references, Structure summary
• Version 1.2: 2015-07-22
  Changes: Database references, Structure summary
• Version 1.3: 2017-11-01
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description