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- PDB-10xa: Nocardia asteroides DnaA DI in the P31(1)21 space group -

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Basic information

Entry
Database: PDB / ID: 10xa
TitleNocardia asteroides DnaA DI in the P31(1)21 space group
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
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesNocardia asteroides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5852
Polymers10,4891
Non-polymers961
Water3,891216
1
A: Chromosomal replication initiator protein DnaA
hetero molecules

A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1704
Polymers20,9782
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)46.751, 46.751, 88.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-252-

HOH

21A-333-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10488.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia asteroides (bacteria) / Gene: dnaA, NCAST_27_00250 / Production host: Escherichia coli (E. coli) / References: UniProt: U5EFM3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1260 mM ammonium sulfate; 100 mM Tris base/hydrochloric acid, pH 8.5; 200 mM Lithium Sulfate

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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: Apr 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.25→23.38 Å / Num. obs: 31853 / % possible obs: 99.9 % / Redundancy: 21.9 % / Biso Wilson estimate: 10.94 Å2 / CC1/2: 1 / Rpim(I) all: 0.008 / Rrim(I) all: 0.047 / Net I/σ(I): 31.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.3 % / Num. unique obs: 1524 / CC1/2: 0.835 / Rpim(I) all: 0.226 / Rrim(I) all: 0.596

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→23.38 Å / SU ML: 0.1138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 1577 4.99 %
Rwork0.1481 30057 -
obs0.1491 31634 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.92 Å2
Refinement stepCycle: LAST / Resolution: 1.25→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms681 0 5 216 902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119767
X-RAY DIFFRACTIONf_angle_d1.38471062
X-RAY DIFFRACTIONf_chiral_restr0.0979127
X-RAY DIFFRACTIONf_plane_restr0.0152142
X-RAY DIFFRACTIONf_dihedral_angle_d14.3601296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.290.23541370.22712657X-RAY DIFFRACTION98.04
1.29-1.340.28581390.2272713X-RAY DIFFRACTION99.65
1.34-1.390.18781420.15332679X-RAY DIFFRACTION100
1.39-1.450.20551410.15092722X-RAY DIFFRACTION99.62
1.45-1.530.17151410.13142691X-RAY DIFFRACTION99.65
1.53-1.630.1451470.11192742X-RAY DIFFRACTION99.97
1.63-1.750.17361440.11212730X-RAY DIFFRACTION99.97
1.75-1.930.16571460.14952695X-RAY DIFFRACTION98.07
1.93-2.210.1341380.13122715X-RAY DIFFRACTION98.45
2.21-2.780.1561430.14882792X-RAY DIFFRACTION99.46
2.78-23.380.16731590.15412921X-RAY DIFFRACTION99.84

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