5T25 | pdb_00005t25

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

PDB DOI: https://doi.org/10.2210/pdb5T25/pdb

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

Deposited: 2016-08-23 Released: 2017-03-01
Deposition Author(s): Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.
Funding Organization(s): OK-INBRE RPI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 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: 63.63 kDa
Atom Count: 5,096
Modeled Residue Count: 585
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	293	Escherichia coli IAI1	Mutation(s): 0 Gene Names: dapA, ECIAI1_2529 EC: 4.3.3.7
UniProt
Find proteins for B7M7I1 (Escherichia coli O8 (strain IAI1)) Explore B7M7I1 Go to UniProtKB: B7M7I1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7M7I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [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: 1.99 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.158 (Depositor), 0.158 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.647	α = 90
b = 56.385	β = 127.62
c = 101.53	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Funding Organization	Location	Grant Number
OK-INBRE RPI	United States	RS20132225112

Revision History (Full details and data files)

Version 1.0: 2017-03-01
Type: Initial release
Version 1.1: 2017-05-17
Changes: Non-polymer description
Version 1.2: 2018-11-07
Changes: Data collection, Source and taxonomy
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection, Derived calculations

5T25 | pdb_00005t25

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)