5T26 | pdb_00005t26

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

PDB DOI: https://doi.org/10.2210/pdb5T26/pdb

Classification: LYASE
Organism(s): Escherichia coli IAI1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-23 Released: 2016-10-05
Deposition Author(s): Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.207 (Depositor), 0.215 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.

To be published.

Macromolecule Content

Total Structure Weight: 63.79 kDa
Atom Count: 4,966
Modeled Residue Count: 587
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	294	Escherichia coli IAI1	Mutation(s): 0 Gene Names: dapA, ECIAI1_2529 EC: 4.3.3.7
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2 Go to UniProtKB: P0A6L2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
74P Query on 74P	A, B	L-PEPTIDE LINKING	C₁₁ H₁₈ N₂ O₅		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.207 (Depositor), 0.215 (DCC)
R-Value Work: 0.168 (Depositor), 0.179 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.714	α = 90
b = 161.492	β = 90
c = 137.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2017-05-17
Changes: Non-polymer description
Version 1.2: 2017-08-23
Changes: Data collection
Version 1.3: 2018-05-30
Changes: Data collection, Derived calculations
Version 2.0: 2019-08-07
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2019-10-02
Changes: Data collection, Derived calculations
Version 2.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.3: 2023-11-15
Changes: Data collection, Derived calculations