8GEK | pdb_00008gek

Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum

PDB DOI: https://doi.org/10.2210/pdb8GEK/pdb

Classification: LYASE
Organism(s): Candidatus Liberibacter solanacearum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-06 Released: 2024-03-20
Deposition Author(s): Gilkes, J.M., Frampton, R.A., Board, A., Sheen, C.R., Smith, G.R., Dobson, R.C.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum

Gilkes, J.M., Frampton, R.A., Board, A., Sheen, C.R., Smith, G.R., Dobson, R.C.J.

To be published.

Macromolecule Content

Total Structure Weight: 192.23 kDa
Atom Count: 14,458
Modeled Residue Count: 1,776
Deposited Residue Count: 1,776
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	296	Candidatus Liberibacter solanacearum	Mutation(s): 0 Gene Names: dapA EC: 4.3.3.7
UniProt
Find proteins for A0A0F4VK59 (Candidatus Liberibacter solanacearum) Explore A0A0F4VK59 Go to UniProtKB: A0A0F4VK59
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F4VK59
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
VPV Query on VPV	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₃ H₂₂ N₂ O₇		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.112	α = 90
b = 132.92	β = 99.79
c = 154.904	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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.