4IDI

Crystal Structure of Rurm1-related protein from Plasmodium Yoelii, PY06420

PDB DOI: https://doi.org/10.2210/pdb4IDI/pdb

Classification: PROTEIN BINDING
Organism(s): Plasmodium yoelii yoelii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-12-12 Released: 2013-12-25
Deposition Author(s): Wernimont, A.K., Tempel, W., Lew, J., Walker, J., Arrowsmith, C.H., Edwards, A.M., Schapira, M., Bountra, C., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Rurm1-related protein from Plasmodium Yoelii, PY06420

Wernimont, A.K., Tempel, W., Lew, J., Walker, J., Arrowsmith, C.H., Edwards, A.M., Schapira, M., Bountra, C., Hui, R., Artz, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 67.11 kDa
Atom Count: 4,190
Modelled Residue Count: 471
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oryza sativa Rurm1-related	A, B, C, D	144	Plasmodium yoelii yoelii	Mutation(s): 1 Gene Names: PY06420
UniProt
Find proteins for Q7RAS9 (Plasmodium yoelii yoelii) Explore Q7RAS9 Go to UniProtKB: Q7RAS9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7RAS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.228
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.59	α = 90
b = 72.72	β = 92.64
c = 107.51	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
BALBES	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Wernimont, A.K.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.