7SYC | pdb_00007syc

Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7SYC/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-24 Released: 2021-12-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.241 (Depositor), 0.249 (DCC)
R-Value Work:
0.198 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SYC

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

Literature

Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae

DeBouver, N.D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 15.93 kDa
Atom Count: 1,077
Modeled Residue Count: 122
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine-triphosphatase	A	141	Klebsiella pneumoniae subsp. pneumoniae	Mutation(s): 0 Gene Names: mutT, E3U38_03970, NCTC9504_05440, RJA_22585 EC: 3.6.1.55
UniProt
Find proteins for A0A1Y0Q4X2 (Klebsiella pneumoniae subsp. pneumoniae) Explore A0A1Y0Q4X2 Go to UniProtKB: A0A1Y0Q4X2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Y0Q4X2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 0.241 (Depositor), 0.249 (DCC)
R-Value Work: 0.198 (Depositor)
R-Value Observed: 0.202 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.14	α = 90
b = 67.14	β = 90
c = 136	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2021-12-15
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, 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.