1PG8 | pdb_00001pg8

Crystal Structure of L-methionine alpha-, gamma-lyase

PDB DOI: https://doi.org/10.2210/pdb1PG8/pdb

Classification: LYASE
Organism(s): Pseudomonas putida
Mutation(s): No

Deposited: 2003-05-28 Released: 2004-06-08
Deposition Author(s): Allen, T.W., Sridhar, V., Prasad, G.S., Han, Q., Xu, M., Tan, Y., Hoffman, R.M., Ramaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.236 (Depositor)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

To be published.

Macromolecule Content

Total Structure Weight: 173.23 kDa
Atom Count: 12,557
Modeled Residue Count: 1,592
Deposited Residue Count: 1,592
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, C, D	398	Pseudomonas putida	Mutation(s): 0 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for P13254 (Pseudomonas putida) Explore P13254 Go to UniProtKB: P13254
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13254
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	F [auth A], O [auth B], S [auth C], W [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], T [auth C], U [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	E [auth A], N [auth B], R [auth C], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.236 (Depositor)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.83	α = 90
b = 154.64	β = 90
c = 80.79	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-08
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description