6AMY | pdb_00006amy

Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6AMY/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-11 Released: 2017-09-06
Deposition Author(s): Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.255 (Depositor), 0.260 (DCC)
R-Value Work:
0.177 (Depositor), 0.176 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6AMY

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

Edwards, T.E., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 91.84 kDa
Atom Count: 5,661
Modeled Residue Count: 784
Deposited Residue Count: 843
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	A, B, C	281	Acinetobacter baumannii	Mutation(s): 0 Gene Names: dapD EC: 2.3.1.117
UniProt
Find proteins for Q5DL43 (Acinetobacter baumannii) Explore Q5DL43 Go to UniProtKB: Q5DL43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5DL43
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.255 (Depositor), 0.260 (DCC)
R-Value Work: 0.177 (Depositor), 0.176 (DCC)
R-Value Observed: 0.181 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.36	α = 90
b = 83.21	β = 90
c = 148.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-09-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-09-06
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-22
Changes: Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.