7AJO

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the cross-linking reaction intermediate

PDB DOI: https://doi.org/10.2210/pdb7AJO/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-29 Released: 2021-10-06
Deposition Author(s): Batuecas, M.T., Hermoso, J.A.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the cross-linking reaction intermediate

Batuecas, M.T., Hermoso, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 60.8 kDa
Atom Count: 4,494
Modelled Residue Count: 492
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase YcbB	A	523	Vibrio cholerae	Mutation(s): 0 Gene Names: ERS013138_01558, ERS013186_00077, ERS013206_00149
UniProt
Find proteins for Q9KSI8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KSI8 Go to UniProtKB: Q9KSI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KSI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S2K Query on S2K Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(2~{S},6~{S})-2-azanyl-6-[[(4~{R})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]heptanedioic acid C₁₂ H₂₁ N₃ O₇ QIFGMZZTJRULMA-RNJXMRFFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.849	α = 90
b = 102.328	β = 90
c = 113.226	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2017-90030-P

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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 R01GM133198.