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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.202 (Depositor), 0.199 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IEL9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.202 (Depositor), 0.199 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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