7F6X

Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.

PDB DOI: https://doi.org/10.2210/pdb7F6X/pdb

Classification: ISOMERASE
Organism(s): Streptomyces albus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-26 Released: 2022-03-16
Deposition Author(s): Li, T.L., Li, Y.S., Chen, M.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.214
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural and Mechanistic Bases for StnK3 and Its Mutant-MediatedLewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.

Chen, M.H., Li, Y.S., Hsu, N.S., Lin, K.H., Wang, Y.L., Wang, Z.C., Chang, C.F., Lin, J.P., Chang, C.Y., Li, T.L.

(2022) ACS Catal 12: 1945-1956

DOI: https://doi.org/10.1021/acscatal.1c04790

Macromolecule Content

Total Structure Weight: 28 kDa
Atom Count: 1,812
Modelled Residue Count: 229
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin domain-containing protein	A, B	131	Streptomyces albus	Mutation(s): 0 Gene Names: stnK3
UniProt
Find proteins for L7PIL3 (Streptomyces albus) Explore L7PIL3 Go to UniProtKB: L7PIL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L7PIL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3A (Subject of Investigation/LOI) Query on I3A 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]	1H-INDOLE-3-CARBALDEHYDE C₉ H₇ N O OLNJUISKUQQNIM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOA (Subject of Investigation/LOI) Query on GOA Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCOLIC ACID C₂ H₄ O₃ AEMRFAOFKBGASW-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.214
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.909	α = 90
b = 66.909	β = 90
c = 117.036	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-03-16

Deposition Author(s):

Li, T.L.

Li, Y.S.

Chen, M.H.

Revision History (Full details and data files)

Version 1.0: 2022-03-16
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-11-29
Changes: Refinement description

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7F6X

Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.

Structural and Mechanistic Bases for StnK3 and Its Mutant-MediatedLewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)