10XH | pdb_000010xh

Bifidobacterium bifidum DnaA DI

PDB DOI: https://doi.org/10.2210/pdb10XH/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Bifidobacterium bifidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-11 Released: 2026-06-03
Deposition Author(s): Ellis, P.K., Schumacher, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Structures reveal DnaA domain I dimer conserved across Actinomycetes: implications for replication initiation

Ellis, P.K., Schumacher, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 20.2 kDa
Atom Count: 1,481
Modeled Residue Count: 175
Deposited Residue Count: 186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosomal replication initiator protein DnaA	A, B	93	Bifidobacterium bifidum	Mutation(s): 0 Gene Names: dnaA, GBA83_04370
UniProt
Find proteins for A0A0M5KVR3 (Bifidobacterium bifidum) Explore A0A0M5KVR3 Go to UniProtKB: A0A0M5KVR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M5KVR3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.931	α = 90
b = 50.965	β = 120.12
c = 47.724	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Schumacher, M.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM130290
National Science Foundation (NSF, United States)	United States	DGE 2139754

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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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.