5VJY

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

PDB DOI: https://doi.org/10.2210/pdb5VJY/pdb

Classification: HYDROLASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-20 Released: 2017-05-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.176
R-Value Work: 0.142
R-Value Observed: 0.144

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 85.32 kDa
Atom Count: 5,696
Modelled Residue Count: 658
Deposited Residue Count: 775
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTP pyrophosphatase	A, B, C, D, E	155	Naegleria fowleri	Mutation(s): 0
UniProt
Find proteins for A0A1Z0YU86 (Naegleria fowleri) Explore A0A1Z0YU86 Go to UniProtKB: A0A1Z0YU86
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Z0YU86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E]	F [auth A], H [auth B], I [auth C], J [auth D], K [auth E]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.176
R-Value Work: 0.142
R-Value Observed: 0.144
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.64	α = 90
b = 118.64	β = 90
c = 98.98	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2017-05-24
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

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Help and Resources

5VJY

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)