5VUG | pdb_00005vug

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5VUG/pdb

• Classification: Structural genomics, Unknown function
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-19 Released: 2017-06-14 
• Deposition Author(s): Kim, Y., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis

Kim, Y., Li, H., Endres, M., 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: 30.66 kDa 
• Atom Count: 2,354 
• Modeled Residue Count: 268 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv2277c	A	281	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv2277c, MTCY339.33
UniProt
Find proteins for P9WLF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WLF1  Go to UniProtKB:  P9WLF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.269	α = 90
b = 43.878	β = 90
c = 68.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Kim, Y., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary