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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.244 (DCC)
R-Value Work:
0.213 (Depositor), 0.221 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WHR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA Query on 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), 0.244 (DCC)
R-Value Work: 0.213 (Depositor), 0.221 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-30

Deposition Author(s):

Naffin-Olivos, J.L.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.