3R03 | pdb_00003r03

The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum

• PDB DOI: https://doi.org/10.2210/pdb3R03/pdb

• Classification: HYDROLASE
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-07 Released: 2011-05-11 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.286 (Depositor) 
• R-Value Work: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.59 kDa 
• Atom Count: 2,095 
• Modeled Residue Count: 260 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUDIX hydrolase	A, B	144	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A0393 EC: 3.6.1.55
UniProt
Find proteins for Q2RXE7 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RXE7  Go to UniProtKB:  Q2RXE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.286 (Depositor) 
• R-Value Work:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.466	α = 90
b = 107.466	β = 90
c = 50.312	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary