5KR5 | pdb_00005kr5

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

PDB DOI: https://doi.org/10.2210/pdb5KR5/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas
Expression System: Escherichia coli BL21
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.204 (Depositor), 0.211 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 105 kDa
Atom Count: 7,403
Modeled Residue Count: 909
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-aminobutyrate transaminase	A, B	479	Pseudomonas	Mutation(s): 0 EC: 2.6.1.18

Small Molecules

Ligands 3 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] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	D [auth A], E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.242 (DCC)
R-Value Work: 0.204 (Depositor), 0.211 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.451	α = 90
b = 102.538	β = 90
c = 199.781	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: 2017-12-06
Changes: Database references
Version 1.2: 2019-01-30
Changes: Data collection, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description