6MLS

Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from L-tyrosine

PDB DOI: https://doi.org/10.2210/pdb6MLS/pdb

Classification: LYASE
Organism(s): Citrobacter freundii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-27 Released: 2019-10-02
Deposition Author(s): Phillips, R.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.193
R-Value Work: 0.166
R-Value Observed: 0.167

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics

Phillips, R.S., Craig, S., Kovalevsky, A., Gerlits, O., Weiss, K., Iorgu, A.I., Heyes, D.J., Hay, S.

(2020) ACS Catal 10: 1692-1703

DOI: https://doi.org/10.1021/acscatal.9b03967

Macromolecule Content

Total Structure Weight: 104.25 kDa
Atom Count: 8,790
Modelled Residue Count: 910
Deposited Residue Count: 912
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine phenol-lyase	A	456	Citrobacter freundii	Mutation(s): 0 Gene Names: tpl EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii) Explore P31013 Go to UniProtKB: P31013
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31013
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine phenol-lyase	B	456	Citrobacter freundii	Mutation(s): 0 Gene Names: tpl EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii) Explore P31013 Go to UniProtKB: P31013
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31013
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain I [auth B]
0JO Query on 0JO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	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 F [auth A]
CQG Query on CQG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], H [auth A]	pyridin-4-ol C₅ H₅ N O GCNTZFIIOFTKIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A]	C [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.193
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.64	α = 90
b = 133.51	β = 90
c = 143.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-10-02

Deposition Author(s):

Phillips, R.S.

Revision History (Full details and data files)

Version 1.0: 2019-10-02
Type: Initial release
Version 1.1: 2020-04-15
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.3: 2023-11-15
Changes: Data collection