8FOQ | pdb_00008foq

Crystal Structure of Kemp Eliminase 1A53-core with bound transition state analogue

PDB DOI: https://doi.org/10.2210/pdb8FOQ/pdb

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-03 Released: 2024-01-10
Deposition Author(s): Zarifi, N., Asthana, P., Fraser, J.S., Chica, R.A.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canada Foundation for Innovation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Kemp Eliminase 1A53-core with bound transition state analogue

Zarifi, N., Asthana, P., Fraser, J.S., Chica, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 30.19 kDa
Atom Count: 2,305
Modeled Residue Count: 247
Deposited Residue Count: 260
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 1A53-core	A	260	Escherichia coli	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
3NY (Subject of Investigation/LOI) Query on 3NY 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]	5-nitro-1H-benzotriazole C₆ H₄ N₄ O₂ AOCDQWRMYHJTMY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.159 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.003	α = 90
b = 61.003	β = 90
c = 121.977	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
PHASER	phasing
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2016-04831
Canada Foundation for Innovation	Canada	26503

Revision History (Full details and data files)

Version 1.0: 2024-01-10
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.