6D6K | pdb_00006d6k

Structure of polyribonucleotide nucleotidyltransferase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb6D6K/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-04-21 Released: 2018-05-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of polyribonucleotide nucleotidyltransferase from Acinetobacter baumannii

Abendroth, J., Phan, J.N., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 152.72 kDa
Atom Count: 8,614
Modeled Residue Count: 1,095
Deposited Residue Count: 1,410
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A, B	705	Acinetobacter baumannii	Mutation(s): 0 Gene Names: pnp, A388_03473, A7A65_13105, A7M79_05700, A7M90_01190, A7N09_01970, AB895_1857, ABUW_3518, APD06_02100, AZE33_01855... pnp, A388_03473, A7A65_13105, A7M79_05700, A7M90_01190, A7N09_01970, AB895_1857, ABUW_3518, APD06_02100, AZE33_01855, B4R90_00995, B9X95_14475, BGC29_15530, BWP00_17325, CAS83_01330, CBE85_05335, CBI29_00441, CEJ63_09865, CHQ89_05525, CPI82_06995, CUC62_01320, CV949_02160, CV950_09585, CV951_02090, CV952_02080, IX87_16365, LV38_00189 EC: 2.7.7.8
UniProt
Find proteins for B0VLR7 (Acinetobacter baumannii (strain SDF)) Explore B0VLR7 Go to UniProtKB: B0VLR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0VLR7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data: https://doi.org/10.18430/M36D6K

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.69	α = 90
b = 93.69	β = 90
c = 266.61	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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.