6S2R | pdb_00006s2r

Mycobacterial hydrolase 2

• PDB DOI: https://doi.org/10.2210/pdb6S2R/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-21 Released: 2020-07-15 
• Deposition Author(s): Cereija, T.B., Vilela, F., Macedo-Ribeiro, S., Pereira, P.J.B.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Mycobacterial hydrolase 2

Cereija, T.B., Empadinhas, N., Macedo-Ribeiro, S., Pereira, P.J.B.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.77 kDa 
• Atom Count: 4,230 
• Modeled Residue Count: 467 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate phosphatase	A, B	236	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: gpgP, Rv2419c EC: 3.1.3.85 (PDB Primary Data), 3.1.3.70 (PDB Primary Data)
UniProt
Find proteins for P9WIC7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIC7  Go to UniProtKB:  P9WIC7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.953	α = 90
b = 48.83	β = 104.33
c = 93.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Cereija, T.B., Vilela, F., Macedo-Ribeiro, S., Pereira, P.J.B.

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Funding Organization	Location	Grant Number
European Regional Development Fund	Portugal	Norte-01-0145-FEDER-000012

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description