2GUU | pdb_00002guu

crystal structure of Plasmodium vivax orotidine 5-monophosphate decarboxylase with 6-aza-UMP bound

• PDB DOI: https://doi.org/10.2210/pdb2GUU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-01 Released: 2006-05-16 
• Deposition Author(s): Dong, A., Lew, J., Zhao, Y., Sundararajan, E., Wasney, G., Vedadi, M., Koeieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Pai, E.F., Kotra, L., Bochkarev, A., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.236 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Plasmodium vivax orotidine 5-monophosphate decarboxylase with 6-aza-UMP bound

DONG, A., LEW, J., ZHAO, Y., Sundararajan, E., WASNEY, G., VEDADI, M., KOEIERADZKI, I., EDWARDS, A.M., ARROWSMITH, C.H., WEIGELT, J., SUNDSTROM, M., Pai, E.F., Kotra, L., BOCHKAREV, A., HUI, R., AMANI, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 40.49 kDa 
• Atom Count: 2,843 
• Modeled Residue Count: 317 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ODcase	A	353	Plasmodium vivax	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UP6	B [auth A]	6-AZA URIDINE 5'-MONOPHOSPHATE C8 H12 N3 O9 P LRVZOSYMNMNQFR-SHUUEZRQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.236 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.731	α = 90
b = 82.151	β = 90
c = 59.739	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Dong, A., Lew, J., Zhao, Y., Sundararajan, E., Wasney, G., Vedadi, M., Koeieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Pai, E.F., Kotra, L., Bochkarev, A., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, 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