9HAQ | pdb_00009haq

Crystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb9HAQ/pdb

Classification: LYASE
Organism(s): Brevibacterium sandarakinum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-04 Released: 2025-11-12
Deposition Author(s): Kopecny, D., Ferchaud, N., Briozzo, P.
Funding Organization(s): Other government, Ministry of Education, Youth and Sports of the Czech Republic, Other private, Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.278 (Depositor), 0.265 (DCC)
R-Value Work:
0.258 (Depositor), 0.247 (DCC)
R-Value Observed:
0.259 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention

Ferchaud, N., Boyer, A., Odegard, B., Hentati, S., Simonson, T., Machover, D., Kopecny, D., Briozzo, P.

To be published.

Macromolecule Content

Total Structure Weight: 693.35 kDa
Atom Count: 45,304
Modeled Residue Count: 6,148
Deposited Residue Count: 6,611
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A, B, D, F, H A, B, D, F, H, I, J, L, P	413	Brevibacterium sandarakinum	Mutation(s): 0 Gene Names: SAMN04489751_4033 EC: 4.4.1.11 (UniProt), 4.4.1.2 (UniProt)
UniProt
Find proteins for A0A1H1YBL2 (Brevibacterium sandarakinum) Explore A0A1H1YBL2 Go to UniProtKB: A0A1H1YBL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1H1YBL2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	C, E, G, K, M C, E, G, K, M, N, O	413	Brevibacterium sandarakinum	Mutation(s): 0 Gene Names: SAMN04489751_4033 EC: 4.4.1.11 (UniProt), 4.4.1.2 (UniProt)
UniProt
Find proteins for A0A1H1YBL2 (Brevibacterium sandarakinum) Explore A0A1H1YBL2 Go to UniProtKB: A0A1H1YBL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1H1YBL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PY6 (Subject of Investigation/LOI) Query on PY6 Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth G] SDF format, chain V [auth E] SDF format, chain S [auth C] SDF format, chain IA [auth P] SDF format, chain GA [auth O] SDF format, chain FA [auth N] SDF format, chain EA [auth M] SDF format, chain DA [auth K] SDF format, chain AA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain V [auth E] MOL2 format, chain S [auth C] MOL2 format, chain IA [auth P] MOL2 format, chain GA [auth O] MOL2 format, chain FA [auth N] MOL2 format, chain EA [auth M] MOL2 format, chain DA [auth K] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain V [auth E] mmCIF format, chain S [auth C] mmCIF format, chain IA [auth P] mmCIF format, chain GA [auth O] mmCIF format, chain FA [auth N] mmCIF format, chain EA [auth M] mmCIF format, chain DA [auth K] mmCIF format, chain AA [auth I]	AA [auth I] DA [auth K] EA [auth M] FA [auth N] GA [auth O] AA [auth I], DA [auth K], EA [auth M], FA [auth N], GA [auth O], IA [auth P], S [auth C], V [auth E], Y [auth G], Z [auth H]	2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID C₁₄ H₂₃ N₂ O₇ P NHVFCSUYJRWFNW-LBPRGKRZSA-N		Interactions Focus chain AA [auth I] Focus chain DA [auth K] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain IA [auth P] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain DA [auth K] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain IA [auth P] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth H]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain HA [auth P] MOL2 format, chain HA [auth P] mmCIF format, chain HA [auth P]	HA [auth P]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain HA [auth P] Interactions & Density Focus chain HA [auth P]
NLE (Subject of Investigation/LOI) Query on NLE Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain T [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain BA [auth J] MOL2 format, chain W [auth F] MOL2 format, chain T [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain BA [auth J] mmCIF format, chain W [auth F] mmCIF format, chain T [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain BA [auth J]	BA [auth J], Q [auth A], R [auth B], T [auth D], W [auth F]	NORLEUCINE C₆ H₁₃ N O₂ LRQKBLKVPFOOQJ-YFKPBYRVSA-N		Interactions Focus chain BA [auth J] Focus chain Q [auth A] Focus chain R [auth B] Focus chain T [auth D] Focus chain W [auth F] Interactions & Density Focus chain BA [auth J] Focus chain Q [auth A] Focus chain R [auth B] Focus chain T [auth D] Focus chain W [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth D] SDF format, chain CA [auth J] MOL2 format, chain X [auth F] MOL2 format, chain U [auth D] MOL2 format, chain CA [auth J] mmCIF format, chain X [auth F] mmCIF format, chain U [auth D] mmCIF format, chain CA [auth J]	CA [auth J], U [auth D], X [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain U [auth D] Focus chain X [auth F] Interactions & Density Focus chain CA [auth J] Focus chain U [auth D] Focus chain X [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, D, F, H A, B, D, F, H, I, J, L, P	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.278 (Depositor), 0.265 (DCC)
R-Value Work: 0.258 (Depositor), 0.247 (DCC)
R-Value Observed: 0.259 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.832	α = 90
b = 151.945	β = 90
c = 316.557	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data processing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Kopecny, D.

Ferchaud, N.

Briozzo, P.

Funding Organization	Location	Grant Number
Other government		FR 49271QH PHC BARRANDE
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	MOBILITY 8J23FR011
Other private		IMEBATRACA
Agence Nationale de la Recherche (ANR)	France	France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release

9HAQ | pdb_00009haq

Crystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 8.5

Literature

Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2