7DXM | pdb_00007dxm

Crystal structure of DltD

PDB DOI: https://doi.org/10.2210/pdb7DXM/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-01-19 Released: 2021-07-21
Deposition Author(s): Yan, X.X., Zeng, Q., Tian, L.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.216 (Depositor), 0.198 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of an O-acyltransfer Terminal Protein stDltD and Its Implications for dlt Operon-mediated D-alanylation of S. thermophilus.

Zeng, Q., Tian, L.F., Liu, Y.P., Yan, X.X., Xu, W.Q.

(2022) PROG BIOCHEM BIOPHYS 48: 1052-1062

DOI: https://doi.org/10.16476/j.pibb.2021.0020

Macromolecule Content

Total Structure Weight: 183.7 kDa
Atom Count: 12,785
Modeled Residue Count: 1,564
Deposited Residue Count: 1,588
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DltD	A, B, C, D	397	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dltD
UniProt
Find proteins for Q5M4V2 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4V2 Go to UniProtKB: Q5M4V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M4V2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D]	E [auth A], F [auth A], G [auth B], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.216 (Depositor), 0.198 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.273	α = 90
b = 109.92	β = 90
c = 282.377	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2022-08-03
Changes: Database references, Structure summary
Version 1.2: 2023-11-29
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.