2PQV | pdb_00002pqv

Crystal structure of MutT/nudix family protein from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2PQV/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-02 Released: 2007-06-05 
• Deposition Author(s): Chang, C., Binkowski, T.A., Zhou, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.226 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of MutT/nudix family protein from Streptococcus pneumoniae.

Chang, C., Binkowski, T.A., Zhou, M., Abdullah, J., Joachimiak, A.

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 (software)

Macromolecule Content 

• Total Structure Weight: 35.57 kDa 
• Atom Count: 2,900 
• Modeled Residue Count: 302 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/nudix family protein	A, B	154	Streptococcus pneumoniae TIGR4	Mutation(s): 2  Gene Names: SP_0119
UniProt
Find proteins for A0A0H2UMZ7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UMZ7  Go to UniProtKB:  A0A0H2UMZ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 1.63 Å
• R-Value Free:  0.226 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.321	α = 90
b = 64.675	β = 107.01
c = 49.449	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Chang, C., Binkowski, T.A., Zhou, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-06-05
  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: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary