8ZKV | pdb_00008zkv

Crystal structure of mutant catalytic domains of threonine deaminase in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb8ZKV/pdb

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

Deposited: 2024-05-17 Released: 2024-06-12
Deposition Author(s): Khodi, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.183 (Depositor), 0.182 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Dimer-Tetramer Transition Modulates the Allosteric Regulation of Threonine Deaminase

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

To be published.

Macromolecule Content

Total Structure Weight: 143.55 kDa
Atom Count: 10,036
Modeled Residue Count: 1,308
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine dehydratase biosynthetic IlvA	A, B, C, D	330	Escherichia coli K-12	Mutation(s): 6 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04968
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density 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] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.183 (Depositor), 0.182 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.567	α = 90
b = 83.808	β = 112.51
c = 143.245	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

Khodi, S.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release
Version 2.0: 2024-09-04
Type: Coordinate replacement
Reason: Model completeness
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2024-09-18
Changes: Derived calculations

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Help and Resources

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Crystal structure of mutant catalytic domains of threonine deaminase in complex with PLP

Dimer-Tetramer Transition Modulates the Allosteric Regulation of Threonine Deaminase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

8ZKV | pdb_00008zkv