3S1T

Structure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb3S1T/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-16 Released: 2012-06-13
Deposition Author(s): Schuldt, L., Mueller-Dieckmann, J., Weiss, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 ?
R-Value Free: 0.211
R-Value Work: 0.193
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

High-resolution X-ray structure of the regulatory domain of the mycobacterial aspartokinase in complex with threonine

Schuldt, L., Mueller-Dieckmann, J., Weiss, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 40.78 kDa
Atom Count: 2,713
Modelled Residue Count: 325
Deposited Residue Count: 373
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	A, B	181	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ask, MT3812, MTV025.057c, Rv3709c EC: 2.7.2.4
UniProt
Find proteins for P9WPX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX3 Go to UniProtKB: P9WPX3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPX3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	C	11	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 EC: 2.7.2.4
UniProt
Find proteins for P9WPX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX3 Go to UniProtKB: P9WPX3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPX3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THR Query on THR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	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 A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 ?
R-Value Free: 0.211
R-Value Work: 0.193
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 53.7	α = 90
b = 63.43	β = 90
c = 108.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Schuldt, L.

Mueller-Dieckmann, J.

Weiss, M.S.

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3S1T

Structure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis

High-resolution X-ray structure of the regulatory domain of the mycobacterial aspartokinase in complex with threonine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2