7N56 | pdb_00007n56

Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E

PDB DOI: https://doi.org/10.2210/pdb7N56/pdb

Classification: HYDROLASE
Organism(s): Rickettsia prowazekii str. Madrid E
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-06-04 Released: 2021-07-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7N56

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

Literature

Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E

Abendroth, J., Weiss, M.J., Calhoun, B., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 196.9 kDa
Atom Count: 13,371
Modeled Residue Count: 1,606
Deposited Residue Count: 1,824
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	152	Rickettsia prowazekii str. Madrid E	Mutation(s): 0 Gene Names: dut, RP399 EC: 3.6.1.23
UniProt
Find proteins for Q9ZDD2 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZDD2 Go to UniProtKB: Q9ZDD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZDD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain N [auth C] SDF format, chain M [auth B] MOL2 format, chain O [auth F] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] mmCIF format, chain O [auth F] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B]	M [auth B], N [auth C], O [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.37	α = 90
b = 97.39	β = 118.597
c = 100.54	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2021-07-07
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.