7KEM | pdb_00007kem

Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb7KEM/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-11 Released: 2020-11-18
Deposition Author(s): Libreros, G.A., Dias, M.V.B.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.275 (Depositor), 0.275 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis.

Libreros, G.A., Dias, M.V.B.

To be published.

Macromolecule Content

Total Structure Weight: 93.46 kDa
Atom Count: 4,182
Modeled Residue Count: 527
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	408	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0JC Query on 0JC Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] J [auth B] C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	Di-mu-iodobis(ethylenediamine)diplatinum(II) C₄ H₁₆ I₂ N₄ Pt₂ XXLKNYJQAYMQHB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
6CL Query on 6CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	6-CARBOXYLYSINE C₇ H₁₅ N₂ O₄ GMKMEZVLHJARHF-SYDPRGILSA-O		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
DGL Query on DGL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.275 (Depositor), 0.275 (DCC)
R-Value Work: 0.261 (Depositor), 0.260 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.528	α = 90
b = 121.051	β = 90
c = 122.699	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Libreros, G.A.

Dias, M.V.B.

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	2010/15971-3

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2023-10-18
Changes: Advisory, Author supporting evidence, Data collection, Database references, Refinement description

7KEM | pdb_00007kem

Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis

Literature

Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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