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- PDB-10yo: Nocardia pseudobrasiliensis DnaA DI -

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Basic information

Entry
Database: PDB / ID: 10yo
TitleNocardia pseudobrasiliensis 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 speciesNocardia pseudobrasiliensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChavez Orozco, J.G. / Ellis, 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. / Chavez Orozco, J.G. / Schumacher, M.A.
History
DepositionFeb 12, 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
A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5922
Polymers10,4971
Non-polymers951
Water52229
1
A: Chromosomal replication initiator protein DnaA
hetero molecules

A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1844
Polymers20,9942
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Unit cell
Length a, b, c (Å)100.342, 100.342, 100.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-218-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10496.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia pseudobrasiliensis (bacteria) / Gene: dnaA, DFR76_11348 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A370HTC5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8 M sodium phosphate monobasic monohydrate; potassium phosphate dibasic, pH 5.0

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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: Apr 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.8→20.48 Å / Num. obs: 4253 / % possible obs: 99.7 % / Redundancy: 25.8 % / Biso Wilson estimate: 51.66 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.099 / Net I/σ(I): 32.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 605 / CC1/2: 0.982 / Rpim(I) all: 0.159 / Rrim(I) all: 0.824 / % 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: 2.8→20.48 Å / SU ML: 0.3296 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 409 10.15 %
Rwork0.2164 3620 -
obs0.2192 4029 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 5 29 744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024739
X-RAY DIFFRACTIONf_angle_d0.57781017
X-RAY DIFFRACTIONf_chiral_restr0.0425124
X-RAY DIFFRACTIONf_plane_restr0.0055134
X-RAY DIFFRACTIONf_dihedral_angle_d12.1171267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.36631260.33161157X-RAY DIFFRACTION92.5
3.21-4.030.26391280.23831190X-RAY DIFFRACTION94.21
4.04-20.480.19841550.16861273X-RAY DIFFRACTION97.74
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)
10.839701894483-1.17708113213-1.813519119216.993513941780.9669252602064.382764781330.633621837106-1.67830835120.04571401411380.725163507126-0.7263635282241.07251633946-0.308039028594-0.6162851451660.5301343699550.497880816707-0.1814083241880.2732285833290.811151028305-0.1963273051550.545607875273-30.59108336727.71074742831-35.0685523947
21.84210921185-2.63026225091-2.182636581735.922383682616.605213299528.20339797198-0.278526590808-0.0502779998629-0.7063165188082.08195908891-0.2345153180950.1248285243022.57218555269-1.00314466713-0.7295216857481.96905775892-0.139799243495-0.2362123319530.781892609855-0.1601890051430.636697677307-21.62853291730.0706636956393-24.418298417
33.976644643934.514518880921.905937781057.283076219362.812554007264.01704458251.42798901061-0.8879042112960.205737172831.97644999987-1.66563860375-0.323248729378-0.1593926102720.9325119388020.2488287014980.802557256095-0.364681762259-0.33104177860.9241954621750.2025055547061.04882581211-15.87939229545.45322451426-31.9044461765
45.175889407962.775514293920.3007993783294.37552254778-0.1891868137172.588054574270.423299332831-0.4902616274020.6925813098960.320837900283-0.2955051226470.341461663943-0.487186815726-0.00815062311121-0.01613483698960.237937372711-0.1239471297550.1505997696850.336013330695-0.110054130880.442826993676-26.12778917277.58148200885-44.3829865789
56.408265873421.92688892649-3.439434584024.47678001368-2.86624803755.98430094389-0.214957428076-1.01749034149-0.8244311107410.140176792289-0.592489424059-0.6556943771030.5866477786640.5010742513640.676988876780.290784863094-0.0555240125730.08919433414040.4673011768650.1154825701040.442485896777-23.8046629910.605141602684-40.5855446745
66.37923742609-1.66549248864-0.004311375703835.60701976814-0.1462994221123.05165908634-0.294329325254-0.3325658311260.749175605652-0.3710464061630.02540874800170.845556420106-0.0435412127635-0.05786764666810.2215773834360.1707961420670.0997584342512-0.1017493916460.4288057565450.04426658099620.488362378284-27.47000436436.82470704831-49.0051713706
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 4 through 21 )4 - 217 - 24
22chain 'A' and (resid 22 through 27 )22 - 2725 - 30
33chain 'A' and (resid 28 through 33 )28 - 3331 - 36
44chain 'A' and (resid 34 through 58 )34 - 5837 - 61
55chain 'A' and (resid 59 through 84 )59 - 8462 - 87
66chain 'A' and (resid 85 through 96 )85 - 9688 - 99

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