3TK8 | pdb_00003tk8

Structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb3TK8/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-25 Released: 2011-10-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Burkholderia pseudomallei

Clifton, M.C., Gardberg, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 104.14 kDa
Atom Count: 6,593
Modeled Residue Count: 776
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	A, B, C	316	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: dapD, BURPS1710b_2594 EC: 2.3.1.117
UniProt
Find proteins for Q3JR17 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JR17 Go to UniProtKB: Q3JR17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JR17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain D [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain D [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain D [auth A]	D [auth A] K [auth A] L [auth A] O [auth A] P [auth B] D [auth A], K [auth A], L [auth A], O [auth A], P [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Z [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	AA [auth C], M [auth A], N [auth A], U [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33TK8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.257	α = 90
b = 117.796	β = 90
c = 123.574	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations