5D2W | pdb_00005d2w

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 5 Wild Type

PDB DOI: https://doi.org/10.2210/pdb5D2W/pdb

Classification: DE NOVO PROTEIN, LYASE
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-06 Released: 2016-09-07
Deposition Author(s): Jackson, C.J., Hong, N.-S., Carr, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.216 (Depositor), 0.205 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5D2W

Ligand Structure Quality Assessment

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

Literature

evolutionary changes in Kemp Eliminase KE07 - Crystal 5 Wild Type

Hong, N.-S., Jackson, C.J., Carr, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 29.32 kDa
Atom Count: 2,200
Modeled Residue Count: 250
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed kemp eliminase KE07	A	264	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6VP Query on 6VP 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]	5-nitro-2-oxidanyl-benzenecarbonitrile C₇ H₄ N₂ O₃ MPQNPFJBRPRBFF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.216 (Depositor), 0.205 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.126	α = 90
b = 97.126	β = 90
c = 155.513	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.