9HVH | pdb_00009hvh

High-efficiency Kemp eliminases by complete computational design

PDB DOI: https://doi.org/10.2210/pdb9HVH/pdb

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

Deposited: 2024-12-29 Released: 2025-06-11
Deposition Author(s): Listov, D., Dym, O., Vos, E., Hoffka, G., Berg, A., Rogotner, S., Caroline, s., Kamerlin, L., Fleishman, S.J.
Funding Organization(s): Volkswagen Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.203 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

High-efficiency Kemp eliminases by complete computational design

Listov, D., Dym, O., Vos, E., Hoffka, G., Berg, A., Rogotner, S., Caroline, s., Kamerlin, L., Fleishman, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 57.97 kDa
Atom Count: 4,203
Modeled Residue Count: 522
Deposited Residue Count: 526
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	A, B	263	Escherichia	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.203 (Depositor), 0.204 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.844	α = 90
b = 69.555	β = 101.04
c = 79.603	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystalClear	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Fleishman, S.J.

Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	94747

Revision History (Full details and data files)

Version 1.0: 2025-06-11
Type: Initial release

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.