3H6X | pdb_00003h6x

Crystal structure of dUTPase from Streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb3H6X/pdb

Classification: HYDROLASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-04-24 Released: 2010-05-05
Deposition Author(s): Li, G.L., Wang, K.T., Liu, X., Li, L.F., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.205 (Depositor)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3H6X

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

Literature

Structure and activity analysis of dUTP nucleotidohydrolase from Streptococcus mutans

Li, G.L., Wang, K.T., Liu, X., Li, L.F., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 49.17 kDa
Atom Count: 3,696
Modeled Residue Count: 387
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTPase	A, B, C	148	Streptococcus mutans	Mutation(s): 0 Gene Names: dut EC: 3.6.1.23
UniProt
Find proteins for Q8DVY3 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DVY3 Go to UniProtKB: Q8DVY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DVY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205 (Depositor)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.78	α = 90
b = 53.52	β = 113.91
c = 93.14	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-05-23
Changes: Data collection
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.