5YXF | pdb_00005yxf

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105L mutant) in complex with Methionine

• PDB DOI: https://doi.org/10.2210/pdb5YXF/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-05 Released: 2018-12-12 
• Deposition Author(s): Sandeep, C.B., Addlagatta, A.
• Funding Organization(s): Deparment of science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105L mutant) in complex with Methionine

Sandeep, C.B., Addlagatta, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.74 kDa 
• Atom Count: 2,354 
• Modeled Residue Count: 282 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A	319	Mycobacterium tuberculosis H37Ra	Mutation(s): 2  Gene Names: mapB, map, MRA_2886 EC: 3.4.11.18
UniProt
Find proteins for A5U6L5 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U6L5  Go to UniProtKB:  A5U6L5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MET	E [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.302	α = 90
b = 48.326	β = 95.19
c = 56.225	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SCALEPACK	data scaling
Coot	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Sandeep, C.B., Addlagatta, A.

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Funding Organization	Location	Grant Number
Deparment of science and Technology	India	EMR/2015/000461

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description