5IT4 | pdb_00005it4

Crystal structure of Mycobacterium avium SerB2 mutant D343N

• PDB DOI: https://doi.org/10.2210/pdb5IT4/pdb

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


• Deposited: 2016-03-16 Released: 2016-04-27 
• Deposition Author(s): Shree, S., Ramachandran, R.
• Funding Organization(s): Council of Scientific and Industrial Research (CSIR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mycobacterium avium SerB2 mutant D343N (MAV_3907) at pH 6.6

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: 41.81 kDa 
• Atom Count: 3,022 
• Modeled Residue Count: 395 
• 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): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.035	α = 90
b = 109.14	β = 90
c = 134.024	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Shree, S., Ramachandran, R.

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Funding Organization	Location	Grant Number
Council of Scientific and Industrial Research (CSIR)	India	--

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description