6SS1

Kemp Eliminase HG3.17 mutant Q50A, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole

PDB DOI: https://doi.org/10.2210/pdb6SS1/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-09-06 Released: 2020-04-01
Deposition Author(s): Bloch, J.S., Pinkas, D.M., Hilvert, D.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.169
R-Value Work: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency

Kries, H., Bloch, J.S., Bunzel, H.A., Pinkas, D.M., Hilvert, D.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.0c00575

Macromolecule Content

Total Structure Weight: 69.05 kDa
Atom Count: 8,253
Modelled Residue Count: 607
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase HG3.17 Q50A, E47N,N300D Complexed with Transition State Analog 6-Nitrobenzotriazole	A, B	317	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6NT (Subject of Investigation/LOI) Query on 6NT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	6-NITROBENZOTRIAZOLE C₆ H₄ N₄ O₂ AOCDQWRMYHJTMY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 1.10 Å
R-Value Free: 0.169
R-Value Work: 0.145
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.76	α = 90
b = 77.62	β = 90
c = 97.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Bloch, J.S.

Pinkas, D.M.

Hilvert, D.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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Help and Resources

6SS1

Kemp Eliminase HG3.17 mutant Q50A, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole

Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency

Entity ID: 1

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)