5E2C | pdb_00005e2c

Crystal structure of N-terminal domain of cytoplasmic peptidase PepQ from Mycobacterium tuberculosis H37Rv

PDB DOI: https://doi.org/10.2210/pdb5E2C/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis H37Ra
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-30 Released: 2015-10-14
Deposition Author(s): Chang, C., Endres, L., Endres, M., SACCHETTINI, J., JOACHIMIAK, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.186 (Depositor), 0.203 (DCC)
R-Value Work:
0.138 (Depositor), 0.155 (DCC)
R-Value Observed:
0.140 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of N-terminal domain of cytoplasmic peptidase PepQ from Mycobacterium tuberculosis H37Rv

Chang, C., Endres, L., Endres, M., SACCHETTINI, J., JOACHIMIAK, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 27.65 kDa
Atom Count: 2,400
Modeled Residue Count: 260
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro dipeptidase	A, B	132	Mycobacterium tuberculosis H37Ra	Mutation(s): 0 Gene Names: pepQ, MRA_2563
UniProt
Find proteins for A5U5N4 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U5N4 Go to UniProtKB: A5U5N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5U5N4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A, B	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.186 (Depositor), 0.203 (DCC)
R-Value Work: 0.138 (Depositor), 0.155 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.684	α = 90
b = 60.202	β = 90
c = 96.268	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

SACCHETTINI, J.

Midwest Center for Structural Genomics (MCSG)

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary