4QTF | pdb_00004qtf

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

PDB DOI: https://doi.org/10.2210/pdb4QTF/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-07 Released: 2015-07-29
Deposition Author(s): Gokulan, K., Varughese, K.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.213 (Depositor), 0.222 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Khare, S., Cerniglia, C.E., Foley, S.L., Varughese, K.I.

To be published.

Macromolecule Content

Total Structure Weight: 38.59 kDa
Atom Count: 2,776
Modeled Residue Count: 349
Deposited Residue Count: 349
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,d-transpeptidase LdtB	A	349	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ldtB, Rv2518c, RVBD_2518c EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6Y9J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLD Query on MLD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA C₃₇ H₅₉ N₇ O₂₀ UPFMKPIBAIPLHT-RSJSDIDPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
3V5 Query on 3V5 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline C₁₁ H₁₉ N₃ O₄ S SKDDBJCIWUNJNL-XKNYDFJKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.213 (Depositor), 0.222 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.272	α = 90
b = 65.881	β = 90
c = 207.456	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Varughese, K.I.

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2016-08-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary

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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.