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- PDB-10xl: Pseudonocardia thermophila DnaA DI -

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Basic information

Entry
Database: PDB / ID: 10xl
TitlePseudonocardia thermophila 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 speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8172
Polymers18,8172
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.597, 51.823, 35.933
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 15 through 29 or resid 31...
d_2ens_1(chain "B" and (resid 15 through 29 or resid 31...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALGLNGLNAB15 - 2918 - 32
d_12ALAALALEULEUAB31 - 4134 - 44
d_13ALAALALEULEUAB46 - 6349 - 66
d_14ARGARGARGARGAB6568
d_15ILEILEVALVALAB67 - 8570 - 88
d_21VALVALGLNGLNBA15 - 2918 - 32
d_22ALAALALEULEUBA31 - 4134 - 44
d_23ALAALALEULEUBA46 - 6349 - 66
d_24ARGARGARGARGBA6568
d_25ILEILEVALVALBA67 - 8570 - 88

NCS oper: (Code: givenMatrix: (-0.933270330396, 0.27440651025, -0.231748910536), (0.324016043344, 0.364800424832, -0.872888454328), (-0.154984173572, -0.88973126121, -0.42936952473)Vector: 9. ...NCS oper: (Code: given
Matrix: (-0.933270330396, 0.27440651025, -0.231748910536), (0.324016043344, 0.364800424832, -0.872888454328), (-0.154984173572, -0.88973126121, -0.42936952473)
Vector: 9.91023451665, 7.54698401122, 14.6264565488)

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 9408.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: dnaA, SAMN05443637_11290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6VF95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.76 Å3/Da / Density % sol: 30.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 M sodium citrate tribasic; 100 mM imidazole/hydrochloric acid, pH 8.0

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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: Oct 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.65→22.45 Å / Num. obs: 15815 / % possible obs: 100 % / Redundancy: 21.5 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 1 / Rpim(I) all: 0.011 / Rrim(I) all: 0.052 / Net I/σ(I): 36.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 770 / CC1/2: 0.948 / Rpim(I) all: 0.163 / Rrim(I) all: 0.586 / % 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: 1.65→22.45 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 1542 9.79 %
Rwork0.1899 14211 -
obs0.192 15753 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 0 140 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091243
X-RAY DIFFRACTIONf_angle_d1.22111693
X-RAY DIFFRACTIONf_chiral_restr0.0726205
X-RAY DIFFRACTIONf_plane_restr0.0162223
X-RAY DIFFRACTIONf_dihedral_angle_d13.7734459
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.925451421923 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.29361390.2581288X-RAY DIFFRACTION100
1.7-1.760.25941520.24581254X-RAY DIFFRACTION100
1.76-1.830.32441270.2471317X-RAY DIFFRACTION99.93
1.83-1.920.27341410.22251282X-RAY DIFFRACTION99.65
1.92-2.020.24011510.21021270X-RAY DIFFRACTION99.58
2.02-2.150.21531410.18881291X-RAY DIFFRACTION99.93
2.15-2.310.23831340.18221281X-RAY DIFFRACTION99.3
2.31-2.540.21621430.19321297X-RAY DIFFRACTION99.24
2.54-2.910.20151310.19151287X-RAY DIFFRACTION99.44
2.91-3.660.18961440.17431310X-RAY DIFFRACTION99.93
3.67-22.450.17761390.17061334X-RAY DIFFRACTION99.8
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)
15.076504502451.63361333864-1.343234129595.230464586460.8142010403444.936884217350.1040282896710.461356727210.156532685455-0.41325497610.162115730595-1.41632654107-0.5768767525250.5164404361680.4393050661870.194298244699-0.02805812487510.1002319176350.1767797272090.005057960996060.30921058370818.85723761627.9327270822618.6151489111
26.26268014158-1.26318030420.814762421464.362453654164.852999968496.233516246490.833162424732-2.475411434630.9216691744423.95136808227-0.667883382853-0.528965158471.17248678346-0.159671910259-0.01778661245990.870903343882-0.196940245757-0.05774077932840.511093526714-0.1629759273450.53370417811917.31174191270.065420531227228.6816407798
35.8070193266-1.954422834121.051984400064.809291338653.41458719113.61370147590.479159870545-0.0164937210779-0.5962609723690.4008884667280.104088614068-1.759188386780.571621208841.01471377706-0.0204380346740.2231835475930.0302814237423-0.07983441204730.232258487256-0.04183008301740.34051013870719.5151919599-3.3481962137720.3471251456
47.4458293605-5.999505784977.661440494938.9397968532-5.9857993588.3169110738-0.2553626564270.9051765951390.0266979979961-0.2884008908350.09886265074780.0394893717194-0.7151761043560.647309825110.1437111775220.283497448384-0.08165445828430.0380006987730.2850175419650.01765879844150.22404625852811.72788846324.712100100948.90377786421
55.3228484578-1.133810168511.498825400085.45899516541-0.7000204991456.86312796396-0.0709951852656-0.00292253238963-0.2455922826050.139966923923-0.1491564461630.0862281010090.0172527551233-0.1176614441150.1490685116620.0894747504171-0.0166079107530.02537716683360.10381208944-0.03210267868240.08554081470047.70871587715-0.8702288497315.1409205171
64.227358678682.609959581620.6688873949936.10700533179-1.886212840653.46729380170.0746922946284-0.0706452791510.2472059251630.366023962922-0.09531488025140.123832419256-0.115099288639-0.0592840224402-0.04417960812440.09165249757270.008148958866620.02902883784550.161568018396-0.03803623509140.1498906552729.762468517198.9665290300821.5269558269
72.804075866391.724893396351.294169612354.956887836470.8279821783752.02318751098-0.06429723092990.176870271973-0.131966047003-0.380301490024-0.01878000498990.3290989637230.09815953682480.1512626501370.1345558532590.1234707753760.009815311694610.01593548541560.1162628873950.008377817559310.07711880272317.052467453594.2789829858713.0206571398
87.367787999954.669391491124.917555541475.677852642054.737045122248.37506415368-0.4897164528940.3599243882170.27198390971-1.267485951910.2487432670490.244307358866-0.879431305025-0.3333977320590.1970947140590.450822376293-0.000176451419442-0.08219215808030.299754496418-0.01116401970880.273019295534-8.59632607823-1.57306971451-3.91549203867
92.972996762110.985524336618-0.1532155442693.02351815699-0.02008190817573.19523687855-0.07119242699020.164158460698-0.0366660003835-0.4051105852910.07551096838730.2062963605430.0739898329312-0.1786926416840.005057373768880.182301966021-0.0319844275971-0.01483975139960.1368382705530.008154780141060.111984099967-6.04742704253-4.318765546175.72229030568
104.548254295152.11793988531-0.9818353157352.578747113011.262974699482.07119704066-0.08018493765920.523959360198-0.209630183814-0.9429809857160.0893082810943-0.1458288322831.102669665040.237828968396-0.1154652398140.3821901580230.0029165359276-0.004001791039960.216449444645-0.05244794483880.157482738634-0.320251108866-6.19571768368-4.37704452143
111.623946194741.82029180141-1.286972415232.25890713575-2.541535874836.603087546150.2284544648730.3268913055610.346185827726-0.2616220863050.051303401228-0.1249057292220.0831309638407-0.213857990334-0.2379447478030.154247402879-0.01242322136680.03095203248420.1672303202710.01895517207110.09939411483651.75814929022-0.7517022801414.28793598767
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 7 through 21 )BA7 - 211 - 15
22chain 'B' and (resid 22 through 26 )BA22 - 2616 - 20
33chain 'B' and (resid 27 through 34 )BA27 - 3421 - 28
44chain 'B' and (resid 35 through 42 )BA35 - 4229 - 36
55chain 'B' and (resid 43 through 63 )BA43 - 6337 - 57
66chain 'B' and (resid 64 through 75 )BA64 - 7558 - 69
77chain 'B' and (resid 76 through 86 )BA76 - 8670 - 80
88chain 'A' and (resid 8 through 21 )AB8 - 211 - 14
99chain 'A' and (resid 22 through 63 )AB22 - 6315 - 56
1010chain 'A' and (resid 64 through 75 )AB64 - 7557 - 68
1111chain 'A' and (resid 76 through 86 )AB76 - 8669 - 79

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