6WQM | pdb_00006wqm

Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Bartonella henselae

PDB DOI: https://doi.org/10.2210/pdb6WQM/pdb

Classification: TRANSFERASE
Organism(s): Bartonella henselae str. Houston-1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-04-29 Released: 2020-05-13
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6WQM

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

Literature

Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Bartonella henselae

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 191.43 kDa
Atom Count: 13,232
Modeled Residue Count: 1,681
Deposited Residue Count: 1,734
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, D, E A, B, C, D, E, F	289	Bartonella henselae str. Houston-1	Mutation(s): 0 Gene Names: dapD, BH00720 EC: 2.3.1.117
UniProt
Find proteins for Q6G549 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G549 Go to UniProtKB: Q6G549
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6G549
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth D] G [auth A], H [auth A], I [auth A], J [auth B], K [auth D], L [auth D], M [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.253 (Depositor), 0.255 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.207 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.84	α = 90
b = 228.22	β = 120.1
c = 71.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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.