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), 0.189 (DCC)
R-Value Work:
0.159 (Depositor), 0.162 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase 1A53-core	A	260	Escherichia coli	Mutation(s): 0

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), 0.189 (DCC)
R-Value Work: 0.159 (Depositor), 0.162 (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

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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

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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.