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- PDB-10xg: Corynebacterium bovis DnaA DI S89C disulfide-linked dimer -

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Basic information

Entry
Database: PDB / ID: 10xg
TitleCorynebacterium bovis DnaA DI S89C disulfide-linked dimer
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
DnaA, N-terminal domain superfamily / 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 ...DnaA, N-terminal domain superfamily / 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
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesCorynebacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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


Theoretical massNumber of molelcules
Total (without water)10,3811
Polymers10,3811
Non-polymers00
Water2,702150
1
A: Chromosomal replication initiator protein DnaA

A: Chromosomal replication initiator protein DnaA


Theoretical massNumber of molelcules
Total (without water)20,7622
Polymers20,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area960 Å2
ΔGint-12 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.686, 58.686, 93.251
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21A-228-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10380.937 Da / Num. of mol.: 1 / Mutation: S89C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium bovis (bacteria) / Gene: dnaA, CXF48_06640 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R8VTP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 21% (w/v) PEG 3000; 70 mM Tris base/Hydrochloric acid, pH 7.0; 140 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.6→22.31 Å / Num. obs: 13172 / % possible obs: 100 % / Redundancy: 22.8 % / Biso Wilson estimate: 17.93 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.097 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 629 / CC1/2: 0.908 / Rpim(I) all: 0.208 / Rrim(I) all: 0.781 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.31 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1310 10.01 %
Rwork0.1928 11782 -
obs0.1971 13092 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.26 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 0 150 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171745
X-RAY DIFFRACTIONf_angle_d1.58671031
X-RAY DIFFRACTIONf_chiral_restr0.1092129
X-RAY DIFFRACTIONf_plane_restr0.0182134
X-RAY DIFFRACTIONf_dihedral_angle_d12.984274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.28761410.23481271X-RAY DIFFRACTION99.58
1.66-1.740.29841400.29421266X-RAY DIFFRACTION99.29
1.74-1.830.3141440.23051285X-RAY DIFFRACTION99.65
1.83-1.950.2491420.20811279X-RAY DIFFRACTION99.79
1.95-2.10.22661430.19871296X-RAY DIFFRACTION100
2.1-2.310.26321440.17681292X-RAY DIFFRACTION99.86
2.31-2.640.24141470.19221312X-RAY DIFFRACTION99.73
2.64-3.320.21851480.191342X-RAY DIFFRACTION99.73
3.33-22.310.21591610.17371439X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 0.969542684274 Å / Origin y: -22.8181340248 Å / Origin z: -0.758984934147 Å
111213212223313233
T0.125925891257 Å2-0.00768433302981 Å2-0.0108386717387 Å2-0.154449439408 Å2-0.00891535920318 Å2--0.0703186668768 Å2
L3.44919365898 °2-0.162062092854 °2-0.148241111728 °2-2.28295686337 °2-0.461184139715 °2--1.79036133136 °2
S-0.0669960522194 Å °-0.0262572531934 Å °0.170001326086 Å °-0.0843905855941 Å °-0.00756734968615 Å °-0.0757159408123 Å °-0.0851906143088 Å °0.0253589706989 Å °0.0642897966174 Å °
Refinement TLS groupSelection details: all

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