6MPD | pdb_00006mpd

Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from 3-F-L-tyrosine

PDB DOI: https://doi.org/10.2210/pdb6MPD/pdb

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

Deposited: 2018-10-05 Released: 2019-10-16
Deposition Author(s): Phillips, R.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (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

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: 104.45 kDa
Atom Count: 8,814
Modeled Residue Count: 910
Deposited Residue Count: 912
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31013
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine phenol-lyase	B	456	Citrobacter freundii	Mutation(s): 0 EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii) Explore P31013 Go to UniProtKB: P31013
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31013
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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] Interactions & Density 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] Interactions & Density Focus chain F [auth A]
YOF Query on YOF Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	3-FLUOROTYROSINE C₉ H₁₀ F N O₃ VIIAUOZUUGXERI-ZETCQYMHSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
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] Interactions & Density 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 G [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain C [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] Interactions & Density 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: 1.79 Å
R-Value Free: 0.210 (Depositor), 0.212 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.5	α = 90
b = 133.13	β = 90
c = 143.43	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Phillips, R.S.

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2020-04-29
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