5E3K | pdb_00005e3k

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid

PDB DOI: https://doi.org/10.2210/pdb5E3K/pdb

Classification: TRANSFERASE
Organism(s): Toxoplasma gondii ME49
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-10-02 Released: 2016-10-26
Deposition Author(s): Filippova, E.V., Minasov, G., Flores, K., Le, H.V., Silverman, R.B., McLeod, R.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.196 (Depositor), 0.203 (DCC)
R-Value Work:
0.154 (Depositor), 0.166 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid

Filippova, E.V., Minasov, G., Flores, K., Le, H.V., Silverman, R.B., McLeod, R.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 98.65 kDa
Atom Count: 7,614
Modeled Residue Count: 846
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B	441	Toxoplasma gondii ME49	Mutation(s): 0 Gene Names: TGME49_269110 EC: 2.6.1.13
UniProt
Find proteins for S8EY38 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore S8EY38 Go to UniProtKB: S8EY38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S8EY38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5JV Query on 5JV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid C₁₃ H₁₇ N₂ O₇ P HRCALJQKZAULQS-MKMNVTDBSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	G [auth A], I [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] E [auth A] F [auth A] K [auth B] L [auth B] D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] 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 K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	H [auth A], O [auth B], P [auth B]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.196 (Depositor), 0.203 (DCC)
R-Value Work: 0.154 (Depositor), 0.166 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.328	α = 100.72
b = 61.524	β = 92.96
c = 63.555	γ = 108.18

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary