5W7Z | pdb_00005w7z

Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii

PDB DOI: https://doi.org/10.2210/pdb5W7Z/pdb

Classification: TRANSFERASE
Organism(s): Rickettsia conorii str. Malish 7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-06-21 Released: 2017-07-26
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.186 (Depositor), 0.188 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii

Bowatte, K., Conrady, D.G., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 86.93 kDa
Atom Count: 6,962
Modeled Residue Count: 761
Deposited Residue Count: 774
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, B	387	Rickettsia conorii str. Malish 7	Mutation(s): 0 Gene Names: dnaN, RC0583 EC: 2.7.7.7
UniProt
Find proteins for Q92I37 (Rickettsia conorii (strain ATCC VR-613 / Malish 7)) Explore Q92I37 Go to UniProtKB: Q92I37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92I37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.186 (Depositor), 0.188 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.52	α = 90
b = 86.91	β = 115.39
c = 79.51	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2017-10-11
Changes: Derived calculations
Version 1.2: 2024-03-13
Changes: Data collection, Database references
Version 1.3: 2024-04-03
Changes: 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.