5KQT | pdb_00005kqt

Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for New Chemistries

PDB DOI: https://doi.org/10.2210/pdb5KQT/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas sp. AAC
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-06 Released: 2017-07-12
Deposition Author(s): Wilding, M., Newman, J., Peat, T.S., Scott, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.237 (Depositor), 0.242 (DCC)
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Reverse engineering: transaminase biocatalyst development using ancestral sequence reconstruction

Wilding, M., Peat, T.S., Kalyaanamoorthy, S., Newman, J., Scott, C., Jermiin, L.S.

(2017) Green Chemistry 19: 5375

DOI: https://doi.org/10.1039/c7gc02343j

Macromolecule Content

Total Structure Weight: 52.03 kDa
Atom Count: 3,682
Modeled Residue Count: 457
Deposited Residue Count: 479
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-aminoburyrate transaminase	A	479	Pseudomonas sp. AAC	Mutation(s): 0 Gene Names: FG99_14885 EC: 2.6.1.18

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.237 (Depositor), 0.242 (DCC)
R-Value Work: 0.196 (Depositor), 0.204 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.346	α = 90
b = 66.346	β = 90
c = 343.314	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2019-01-30
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description