7JPJ | pdb_00007jpj

Crystal Structure of the essential dimeric LYSA from Phaeodactylum tricornutum

PDB DOI: https://doi.org/10.2210/pdb7JPJ/pdb

Classification: LYASE
Organism(s): Phaeodactylum tricornutum CCAP 1055/1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-08 Released: 2021-06-16
Deposition Author(s): Fedorov, E., Belinski, V.A., Brunson, J.K., Almo, S.C., Dupont, C.L., Ghosh, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.241 (Depositor), 0.245 (DCC)
R-Value Work:
0.197 (Depositor), 0.202 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Phaeodactylum tricornutum diaminopimelate decarboxylase was acquired via horizontal gene transfer from bacteria and displays substrate promiscuity

Bielinski, V.A., Brunson, J.K., Ghosh, A., Moosburner, M.A., Garza, E.A., Fussy, Z., Bai, J., McKinnie, S.M.K., Moore, B.S., Allen, A.E., Almo, S.C., Dupont, C.L.

(2020) bioRxiv

DOI: https://doi.org/10.1101/2020.10.01.322594

Macromolecule Content

Total Structure Weight: 94.58 kDa
Atom Count: 6,563
Modeled Residue Count: 866
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
Diaminopimelate decarboxylase	A, B	441	Phaeodactylum tricornutum CCAP 1055/1	Mutation(s): 0 Gene Names: PHATRDRAFT_21592
UniProt
Find proteins for B7G3A2 (Phaeodactylum tricornutum (strain CCAP 1055/1)) Explore B7G3A2 Go to UniProtKB: B7G3A2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7G3A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DLY (Subject of Investigation/LOI) Query on DLY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	D-LYSINE C₆ H₁₄ N₂ O₂ KDXKERNSBIXSRK-RXMQYKEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [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 G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]