1UKJ | pdb_00001ukj

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb1UKJ/pdb

Classification: LYASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-08-24 Released: 2004-10-19
Deposition Author(s): Misaki, S., Takimoto, A., Takakura, T., Yoshioka, T., Yamashita, M., Tamura, T., Tanaka, H., Inagaki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.295 (Depositor)
R-Value Work:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Detailed structure of L-Methionine -Lyase from Pseudomonas putida

Misaki, S., Takimoto, A., Takakura, T., Yoshioka, T., Yamashita, M., Tamura, T., Tanaka, H., Inagaki, K.

To be published.

Macromolecule Content

Total Structure Weight: 172.09 kDa
Atom Count: 13,148
Modeled Residue Count: 1,592
Deposited Residue Count: 1,592
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B, C, D	398	Pseudomonas putida	Mutation(s): 1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.295 (Depositor)
R-Value Work: 0.177 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.093	α = 90
b = 133.093	β = 90
c = 215.028	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-19
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

1UKJ | pdb_00001ukj

Detailed structure of L-Methionine-Lyase from Pseudomonas putida

Literature

Detailed structure of L-Methionine -Lyase from Pseudomonas putida

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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