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- PDB-10xd: Rhodococcus ruber DnaA DI -

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Basic information

Entry
Database: PDB / ID: 10xd
TitleRhodococcus ruber 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
DnaA, N-terminal domain superfamily / 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 ...DnaA, N-terminal domain superfamily / 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 speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)10,0461
Polymers10,0461
Non-polymers00
Water1,56787
1
A: Chromosomal replication initiator protein DnaA

A: Chromosomal replication initiator protein DnaA


Theoretical massNumber of molelcules
Total (without water)20,0932
Polymers20,0932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)63.904, 63.904, 63.272
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10046.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Gene: dnaA, RHRU231_590005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A098BQE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.3 M Ammonium citrate tribasic dihydrate, pH 7.0; 0.1M Bis-tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.95→31.95 Å / Num. obs: 11280 / % possible obs: 100 % / Redundancy: 17.5 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.07 / Net I/σ(I): 23.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 18.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 807 / CC1/2: 0.909 / Rpim(I) all: 0.361 / Rrim(I) all: 1.576 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→31.95 Å / SU ML: 0.2924 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 537 4.94 %
Rwork0.2011 10329 -
obs0.203 10866 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 0 87 780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152724
X-RAY DIFFRACTIONf_angle_d1.4074989
X-RAY DIFFRACTIONf_chiral_restr0.0836113
X-RAY DIFFRACTIONf_plane_restr0.016129
X-RAY DIFFRACTIONf_dihedral_angle_d16.21259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.150.34251350.322509X-RAY DIFFRACTION95.83
2.15-2.460.29531260.25512497X-RAY DIFFRACTION93.98
2.46-3.090.28161320.26922581X-RAY DIFFRACTION96.93
3.1-31.950.20671440.15862742X-RAY DIFFRACTION99.07
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3711486298290.000980546971435-0.554101473480.2784951451020.1689200439170.940021581435-0.961923044938-1.416662970111.396263130380.9747752265521.266623064141.654407404410.00502767946655-1.75202848309-0.3522512335141.273084325760.03132447116440.3898690149851.97738540641-0.05125126043121.4667856258212.138443161-5.5089199076830.0211526491
26.263937027220.923863605486-1.318519455325.890591189743.440502843977.474585828-0.632814528433-0.6564390933590.09801640803770.6398502725150.09642019900810.1756276592190.2556458724520.7285621141610.4176742807090.4550700923950.03109614155730.04608480063760.3828418355860.003618207810230.30599133041429.203631685-17.111674318824.5955926686
37.8190543979-1.01411888812-0.07796217396726.913671186684.618250250656.194316005010.086502705961-0.03034829586840.3621515931810.0416970595398-0.272925153170.146579402309-0.017508418659-0.1868620476450.1691501184460.363294853856-0.0418699334072-0.02267594931630.2874861488470.01676489446840.35828568245718.8837806474-20.285235743619.6217061119
47.63120110292-0.4046713916532.48230726147.756940753815.011247394074.22865489844-0.0143411028005-1.223674984940.7031796586811.724340405530.2349627005110.3937656778270.840290814721-0.0179515809433-0.1638558493240.60320177037-0.07217179935580.1013874663950.462870690417-0.1439845207170.39363794881121.0458156621-17.15525266531.7029695103
58.012076427090.5385930515732.429217018.144628756585.38406710554.098172754420.2208073021480.1206460727321.00989545017-0.317513595238-0.6392416504051.0605936197-1.87656620975-0.7368531174080.9089599559680.574929128549-0.0235034591815-0.07317185501360.313686270087-0.06307468044060.61025752034615.4545148172-17.453068991321.3863128699
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 6 )-2 - 61 - 9
22chain 'A' and (resid 7 through 36 )7 - 3610 - 39
33chain 'A' and (resid 37 through 64 )37 - 6440 - 67
44chain 'A' and (resid 65 through 76 )65 - 7668 - 79
55chain 'A' and (resid 77 through 90 )77 - 9080 - 93

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