2PLW | pdb_00002plw

Crystal structure of a ribosomal RNA methyltransferase, putative, from Plasmodium falciparum (PF13_0052).

• PDB DOI: https://doi.org/10.2210/pdb2PLW/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2007-05-08 
• Deposition Author(s): Wernimont, A.K., Hassanali, A., Lin, L., Lew, J., Zhao, Y., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Hui, R., Qiu, W., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a ribosomal RNA methyltransferase, putative, from Plasmodium falciparum (PF13_0052).

Wernimont, A.K., Hassanali, A., Lin, L., Lew, J., Zhao, Y., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Hui, R., Qiu, W.

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: 23.87 kDa 
• Atom Count: 1,659 
• Modeled Residue Count: 182 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA methyltransferase, putative	A	201	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF13_0052 EC: 2.1.1
UniProt
Find proteins for Q8IEL9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEL9  Go to UniProtKB:  Q8IEL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.595	α = 90
b = 59.798	β = 90
c = 71.295	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Wernimont, A.K., Hassanali, A., Lin, L., Lew, J., Zhao, Y., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Hui, R., Qiu, W., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description