7M7C | pdb_00007m7c

Crystal Structure of Hip1 (Rv2224c) mutant - T466A/S228DHA (dehydroalanine)

• PDB DOI: https://doi.org/10.2210/pdb7M7C/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-03-27 Released: 2022-03-30 
• Deposition Author(s): Naffin-Olivos, J.L., Daab, A., Goldfarb, N.E., Doran, M.H., Baikovitz, J., Liu, D., Sun, S., White, A., Dunn, B.M., Rengarajan, J., Petsko, G.A., Ringe, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Inhibitors and Inactivators of Mycobacterium tuberculosis serine protease Hip1 (Rv2224c)

Naffin-Olivos, J.L., Daab, A., Goldfarb, N., Doran, M.H., Baikovitz, J., Liu, D., Sun, S., White, A., Dunn, B.M., Rengarajan, J., Petsko, G.A., Ringe, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.94 kDa 
• Atom Count: 3,498 
• Modeled Residue Count: 463 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase A	A	492	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: caeA, Rv2224c, MTCY427.05c EC: 3.1.1 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P9WHR3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHR3  Go to UniProtKB:  P9WHR3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.75	α = 90
b = 104.75	β = 90
c = 128.309	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Naffin-Olivos, J.L., Daab, A., Goldfarb, N.E., Doran, M.H., Baikovitz, J., Liu, D., Sun, S., White, A., Dunn, B.M., Rengarajan, J., Petsko, G.A., Ringe, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM32415

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description