5JLP | pdb_00005jlp

Crystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain

• PDB DOI: https://doi.org/10.2210/pdb5JLP/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium avium 104
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-04-27 Released: 2017-05-03 
• Deposition Author(s): Shree, S., Ramachandran, R.
• Funding Organization(s): CSIR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain

Shree, S., Ramachandran, R.

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: 42.1 kDa 
• Atom Count: 2,849 
• Modeled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphatase	A	396	Mycobacterium avium 104	Mutation(s): 1  Gene Names: serB, MAV_3907 EC: 3.1.3.3
UniProt
Find proteins for A0QJI1 (Mycobacterium avium (strain 104)) Explore A0QJI1  Go to UniProtKB:  A0QJI1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG0	C [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
SER	E [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.548	α = 90
b = 109.535	β = 90
c = 134.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Shree, S., Ramachandran, R.

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Funding Organization	Location	Grant Number
CSIR	India	--

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description