8KH3 | pdb_00008kh3

Crystal Structure of Kemp Eliminase HG3.17 in complexed with 5-cyanobenzotriazole

PDB DOI: https://doi.org/10.2210/pdb8KH3/pdb

Classification: LYASE
Organism(s): Thermoascus aurantiacus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-21 Released: 2024-09-04
Deposition Author(s): Bunzel, A., Mori, T., Hilvert, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.145 (Depositor), 0.145 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Evolution of preorganized electric fields boosts catalysis in a designer enzyme

Bunzel, A., Schneider, S.H., Kozuch, J.A., Mori, T., Boxer, S.G., Mulholland, A.J., Hilvert, D.

To be published.

Macromolecule Content

Total Structure Weight: 34.7 kDa
Atom Count: 2,596
Modeled Residue Count: 299
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase HG3.17	A	318	Thermoascus aurantiacus	Mutation(s): 0 EC: 3.2.1.8
UniProt
Find proteins for P23360 (Thermoascus aurantiacus) Explore P23360 Go to UniProtKB: P23360
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23360
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VWF (Subject of Investigation/LOI) Query on VWF 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]	1H-benzotriazole-5-carbonitrile C₇ H₄ N₄ OEBMOZBCDOBXAN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.191 (Depositor), 0.192 (DCC)
R-Value Work: 0.145 (Depositor), 0.145 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.968	α = 90
b = 57.553	β = 90
c = 91.516	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.