3GOS | pdb_00003gos

The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb3GOS/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-19 Released: 2009-05-12
Deposition Author(s): Zhang, R., Maltseva, N., Kwon, K., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.272 (Depositor), 0.285 (DCC)
R-Value Work:
0.227 (Depositor), 0.232 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Yersinia pestis CO92

Zhang, R., Maltseva, N., Kwon, K., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 90.58 kDa
Atom Count: 6,574
Modeled Residue Count: 822
Deposited Residue Count: 828
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	276	Yersinia pestis	Mutation(s): 0 Gene Names: dapD, gi: 16121341, y3140, YPO1041, YP_2810 EC: 2.3.1.117
UniProt
Find proteins for Q8ZH69 (Yersinia pestis) Explore Q8ZH69 Go to UniProtKB: Q8ZH69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZH69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.272 (Depositor), 0.285 (DCC)
R-Value Work: 0.227 (Depositor), 0.232 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.792	α = 90
b = 69.695	β = 105.28
c = 106.448	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MERLOT	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, 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.