6LD8 | pdb_00006ld8

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine

PDB DOI: https://doi.org/10.2210/pdb6LD8/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-11-20 Released: 2020-11-25
Deposition Author(s): Ngo, H.P.T., Nguyen, T.D.Q., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (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

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine

Ngo, H.P.T., Nguyen, T.D.Q., Kang, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 174.26 kDa
Atom Count: 12,208
Modeled Residue Count: 1,549
Deposited Residue Count: 1,632
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 gamma-synthase	A, B, C, D	408	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 1 Gene Names: metB, XOO1818
UniProt
Find proteins for Q5H1U9 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H1U9 Go to UniProtKB: Q5H1U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5H1U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0JO (Subject of Investigation/LOI) Query on 0JO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid C₁₁ H₁₃ N₂ O₇ P BHIGINKEEFZJGX-YIXHJXPBSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CYS (Subject of Investigation/LOI) Query on CYS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	F [auth A], H [auth B], J [auth C], L [auth D]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]