7KG9 | pdb_00007kg9

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KG9/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-10-16 Released: 2021-10-20
Deposition Author(s): Saran, S., Majdi Yazdi, M., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.331 (Depositor), 0.331 (DCC)
R-Value Work:
0.275 (Depositor), 0.276 (DCC)
R-Value Observed:
0.278 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KG9

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

Literature

Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni

Majdi Yazd, M., Reddy Annadi, K., Saran, S., Bhagwat, A., Sanders, D.A.R., Palmer, D.R.J.

To be published.

Macromolecule Content

Total Structure Weight: 209.29 kDa
Atom Count: 14,779
Modeled Residue Count: 1,784
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 1 Gene Names: dapA, Cj0806 EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain MA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain MA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain MA [auth D]	MA [auth D], W [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Focus chain W [auth B] Interactions & Density Focus chain MA [auth D] Focus chain W [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain TA [auth F] SDF format, chain SA [auth F] SDF format, chain J [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain J [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain J [auth A]	J [auth A], SA [auth F], TA [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain SA [auth F] Focus chain TA [auth F] Interactions & Density Focus chain J [auth A] Focus chain SA [auth F] Focus chain TA [auth F]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth E] SDF format, chain X [auth B] SDF format, chain YA [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth F]	FA [auth C] M [auth A] NA [auth D] OA [auth E] X [auth B] FA [auth C], M [auth A], NA [auth D], OA [auth E], X [auth B], YA [auth F]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain FA [auth C] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth E] Focus chain X [auth B] Focus chain YA [auth F] Interactions & Density Focus chain FA [auth C] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth E] Focus chain X [auth B] Focus chain YA [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain U [auth B] SDF format, chain LA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain LA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain LA [auth D]	EA [auth C] K [auth A] LA [auth D] U [auth B] WA [auth F] EA [auth C], K [auth A], LA [auth D], U [auth B], WA [auth F], XA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain U [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Interactions & Density Focus chain EA [auth C] Focus chain K [auth A] Focus chain LA [auth D] Focus chain U [auth B] Focus chain WA [auth F] Focus chain XA [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B]	L [auth A], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain RA [auth F] SDF format, chain Z [auth C] SDF format, chain R [auth B] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain IA [auth D] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	AA [auth C] BA [auth C] CA [auth C] G [auth A] GA [auth D] AA [auth C], BA [auth C], CA [auth C], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], O [auth B], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Y [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B]	N [auth A], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain Y [auth B] Interactions & Density Focus chain N [auth A] Focus chain Y [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain JA [auth D] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain S [auth B] SDF format, chain KA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain KA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain KA [auth D]	DA [auth C] JA [auth D] KA [auth D] S [auth B] T [auth B] DA [auth C], JA [auth D], KA [auth D], S [auth B], T [auth B], UA [auth F], VA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Interactions & Density Focus chain DA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain VA [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI Query on KPI	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.331 (Depositor), 0.331 (DCC)
R-Value Work: 0.275 (Depositor), 0.276 (DCC)
R-Value Observed: 0.278 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.83	α = 90
b = 225.17	β = 90
c = 200.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
AMPLE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Majdi Yazdi, M.

Sanders, D.A.R.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-29
Changes: Data collection

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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.