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- PDB-10xe: Corynebacterium diphtheriae DnaA DI -

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Basic information

Entry
Database: PDB / ID: 10xe
TitleCorynebacterium diphtheriae DnaA DI
ComponentsChromosomal replication initiator protein DnaA
KeywordsDNA BINDING PROTEIN / Initiator
Function / homology
Function and homology information


regulation of DNA replication / DNA replication origin binding / DNA replication initiation / lipid binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Chromosomal replication control, initiator DnaA, conserved site / DnaA protein signature. / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Bacterial dnaA protein helix-turn-helix / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator ...Chromosomal replication control, initiator DnaA, conserved site / DnaA protein signature. / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Bacterial dnaA protein helix-turn-helix / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / PHOSPHATE ION / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsEllis, P.K. / Schumacher, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
National Science Foundation (NSF, United States)DGE 2139754 United States
CitationJournal: To Be Published
Title: Structures reveal DnaA domain I dimer conserved across Actinomycetes: implications for replication initiation
Authors: Ellis, P.K. / Schumacher, M.A.
History
DepositionFeb 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosomal replication initiator protein DnaA
B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1419
Polymers20,6442
Non-polymers4977
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-20 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.682, 54.982, 55.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10321.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: dnaA, DIP0001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NKL7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 800 mM potassium phosphate dibasic; 100 mM HEPES/sodium hydroxide, pH 7.5; 800 mM sodium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.96→37.12 Å / Num. obs: 87895 / % possible obs: 93.9 % / Redundancy: 25.5 % / Biso Wilson estimate: 10.89 Å2 / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.063 / Net I/σ(I): 26.4
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3100 / CC1/2: 0.33 / Rpim(I) all: 0.345 / Rrim(I) all: 1.599 / % possible all: 68.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→37.12 Å / SU ML: 0.0948 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.5633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.162 2011 2.29 %
Rwork0.1413 85696 -
obs0.1418 87707 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 0.96→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 23 322 1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051750
X-RAY DIFFRACTIONf_angle_d1.18962423
X-RAY DIFFRACTIONf_chiral_restr0.0901269
X-RAY DIFFRACTIONf_plane_restr0.0133320
X-RAY DIFFRACTIONf_dihedral_angle_d12.934681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.980.33281010.32014569X-RAY DIFFRACTION70.34
0.98-1.010.28431420.26685787X-RAY DIFFRACTION89.6
1.01-1.040.21991430.22126012X-RAY DIFFRACTION92.35
1.04-1.070.22041420.19426012X-RAY DIFFRACTION92.85
1.07-1.110.19351370.14866086X-RAY DIFFRACTION93.8
1.11-1.160.18881460.13496143X-RAY DIFFRACTION94.51
1.16-1.210.14051480.11976200X-RAY DIFFRACTION95.14
1.21-1.270.16221500.1236187X-RAY DIFFRACTION94.81
1.27-1.350.17061430.12226225X-RAY DIFFRACTION95.49
1.35-1.460.14631440.11076329X-RAY DIFFRACTION96.58
1.46-1.60.13731490.10996364X-RAY DIFFRACTION96.56
1.6-1.840.1531550.12146461X-RAY DIFFRACTION98.06
1.84-2.310.14481530.1366509X-RAY DIFFRACTION97.78
2.31-37.120.15981580.14896812X-RAY DIFFRACTION98.74

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