9JFI | pdb_00009jfi

Structure of wild type catalytic domains of threonine deaminase in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb9JFI/pdb
Entry: 9JFI supersedes: 8ZLV

Classification: STRUCTURAL PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-09-04 Released: 2025-05-14
Deposition Author(s): Khodi, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.224 (Depositor), 0.223 (DCC)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Dimer-Tetramer Transition Modulates the allosteric regulation of Threonine Deaminase

Khodi, S., Yekeen, H., Liu, H., Chen, Q.

To be published.

Macromolecule Content

Total Structure Weight: 70.39 kDa
Atom Count: 4,842
Modeled Residue Count: 642
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine dehydratase biosynthetic IlvA	A, B	327	Escherichia coli K-12	Mutation(s): 3 Gene Names: ilvA, b3772, JW3745 EC: 4.3.1.19
UniProt
Find proteins for P04968 (Escherichia coli (strain K12)) Explore P04968 Go to UniProtKB: P04968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04968
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.224 (Depositor), 0.223 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.159	α = 90
b = 102.159	β = 90
c = 116.473	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

This entry supersedes: 8ZLV

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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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.