2YHK | pdb_00002yhk

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii

PDB DOI: https://doi.org/10.2210/pdb2YHK/pdb

Classification: LYASE
Organism(s): Citrobacter freundii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-05-03 Released: 2012-05-02
Deposition Author(s): Milic, D., Demidkina, T.V., Matkovic-Calogovic, D., Antson, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.177 (Depositor), 0.195 (DCC)
R-Value Work:
0.156 (Depositor), 0.177 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Citrobacter Freundii Asp214Ala Tyrosine Phenol-Lyase Reveals that Asp214 is Critical for Maintaining a Strain in the Internal Aldimine

Milic, D., Demidkina, T.V., Zakomirdina, L.N., Matkovic-Calogovic, D., Antson, A.A.

(2012) Croat Chem Acta 85: 283

DOI: https://doi.org/10.5562/CCA1915

Macromolecule Content

Total Structure Weight: 104.78 kDa
Atom Count: 8,157
Modeled Residue Count: 910
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE PHENOL-LYASE	A, B	456	Citrobacter freundii	Mutation(s): 1 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 K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.177 (Depositor), 0.195 (DCC)
R-Value Work: 0.156 (Depositor), 0.177 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.605	α = 90
b = 142.705	β = 90
c = 59.412	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Milic, D.

Demidkina, T.V.

Matkovic-Calogovic, D.

Antson, A.A.

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2012-11-28
Changes: Database references
Version 1.2: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary

2YHK | pdb_00002yhk

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii

Literature

Crystal Structure of Citrobacter Freundii Asp214Ala Tyrosine Phenol-Lyase Reveals that Asp214 is Critical for Maintaining a Strain in the Internal Aldimine

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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