6D47 | pdb_00006d47

Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Mycobacterium marinum

PDB DOI: https://doi.org/10.2210/pdb6D47/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycobacterium marinum M
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-17 Released: 2018-05-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.226 (Depositor), 0.231 (DCC)
R-Value Work:
0.193 (Depositor), 0.201 (DCC)
R-Value Observed:
0.195 (Depositor)

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

Literature

Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Mycobacterium marinum

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 43.35 kDa
Atom Count: 2,963
Modeled Residue Count: 388
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A	410	Mycobacterium marinum M	Mutation(s): 0 Gene Names: dnaN, MMAR_0002
UniProt
Find proteins for B2HI47 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HI47 Go to UniProtKB: B2HI47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2HI47
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.226 (Depositor), 0.231 (DCC)
R-Value Work: 0.193 (Depositor), 0.201 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.41	α = 90
b = 137.41	β = 90
c = 83.08	γ = 120

Software Package:

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

Structure Validation

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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

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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.