7RZM | pdb_00007rzm

Crystal Structure of dnaN DNA polymerase III beta subunit from Stenotrophomonas maltophilia K279a

PDB DOI: https://doi.org/10.2210/pdb7RZM/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-27 Released: 2021-10-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of dnaN DNA polymerase III beta subunit from Stenotrophomonas maltophilia K279a

Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 41.84 kDa
Atom Count: 3,199
Modeled Residue Count: 367
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A	374	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: dnaN, Smlt0002
UniProt
Find proteins for B2FT80 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FT80 Go to UniProtKB: B2FT80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2FT80
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.96	α = 90
b = 160.96	β = 90
c = 36.15	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 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.