6CJA | pdb_00006cja

Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine

PDB DOI: https://doi.org/10.2210/pdb6CJA/pdb

Classification: LYASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-02-26 Released: 2018-03-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.168 (Depositor), 0.170 (DCC)
R-Value Work:
0.141 (Depositor), 0.140 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: other
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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 Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 174.2 kDa
Atom Count: 13,874
Modeled Residue Count: 1,524
Deposited Residue Count: 1,564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase	A, B, C, D	391	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: metC, lpg0890 EC: 4.4.1.8
UniProt
Find proteins for Q5ZX43 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZX43 Go to UniProtKB: Q5ZX43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZX43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F0G Query on F0G Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], I [auth B], K [auth C], N [auth D]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine C₁₁ H₁₅ N₂ O₇ P UPOKXKNJCNHZTH-ASMSWWRESA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], H [auth A], L [auth C], O [auth D]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain O [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C]