2NX8

The crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

PDB DOI: https://doi.org/10.2210/pdb2NX8/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pyogenes serotype M6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-11-17 Released: 2007-08-21
Deposition Author(s): Hwang, K.Y., Lee, W.-H., Kim, Y.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.214
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

Lee, W.-H., Kim, Y.K., Nam, K.H., Priyadarshi, A., Lee, E.H., Kim, E.E., Jeon, Y.H., Cheong, C., Hwang, K.Y.

(2007) Proteins 68: 1016-1019

PubMed: 17554781 Search on PubMed
DOI: https://doi.org/10.1002/prot.21456
Primary Citation of Related Structures:
2NX8

Organizational Affiliation

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea.

Macromolecule Content

Total Structure Weight: 20.4 kDa
Atom Count: 1,470
Modelled Residue Count: 168
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNA-specific adenosine deaminase	A	179	Streptococcus pyogenes serotype M6	Mutation(s): 2 EC: 3.5.4
UniProt
Find proteins for Q5XE14 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XE14 Go to UniProtKB: Q5XE14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5XE14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.214
R-Value Observed: 0.214
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.091	α = 90
b = 80.091	β = 90
c = 81.104	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-08-21

Deposition Author(s):

Hwang, K.Y.

Lee, W.-H.

Kim, Y.K.

Revision History (Full details and data files)

Version 1.0: 2007-08-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-12-27
Changes: Data collection

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Help and Resources

2NX8

The crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)