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- PDB-10xo: Streptomyces lividans DnaA DI protein in the P6(1)22 space group -

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Basic information

Entry
Database: PDB / ID: 10xo
TitleStreptomyces lividans DnaA DI protein in the P6(1)22 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
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 speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)10,1923
Polymers10,0651
Non-polymers1282
Water86548
1
A: Chromosomal replication initiator protein DnaA
hetero molecules

A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3846
Polymers20,1292
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area1870 Å2
ΔGint-26 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.460, 57.460, 99.032
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

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10064.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: dnaA, SLI_4136 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9DVX7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.2 M sodium chloride; 0.1 M sodium acetate trihydrate, pH 4.6

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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: May 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→22.23 Å / Num. obs: 7049 / % possible obs: 99.9 % / Redundancy: 161.5 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.006 / Rrim(I) all: 0.072 / Net I/σ(I): 85
Reflection shellResolution: 2→2.05 Å / Redundancy: 146.7 % / Mean I/σ(I) obs: 8.1 / Num. unique obs: 510 / CC1/2: 0.989 / Rpim(I) all: 0.091 / Rrim(I) all: 1.105 / % 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→22.23 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 683 10.01 %
Rwork0.2283 6143 -
obs0.232 6826 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.73 Å2
Refinement stepCycle: LAST / Resolution: 2→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms628 0 7 48 683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036674
X-RAY DIFFRACTIONf_angle_d0.6778920
X-RAY DIFFRACTIONf_chiral_restr0.0473107
X-RAY DIFFRACTIONf_plane_restr0.0071121
X-RAY DIFFRACTIONf_dihedral_angle_d15.7583254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.37161260.30051136X-RAY DIFFRACTION93.34
2.15-2.370.25941340.26191202X-RAY DIFFRACTION97.8
2.37-2.710.27841350.25151219X-RAY DIFFRACTION98.26
2.71-3.420.25261380.23611233X-RAY DIFFRACTION97.79
3.42-22.230.24871500.19831353X-RAY DIFFRACTION99.08
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)
15.331178124710.1441756421010.509747557022.92744764683-1.121184422984.14869166028-0.13365053867-0.7942379612060.7414848330650.40940768069-0.125823366144-0.104810912854-0.4586147674420.1869279443420.1878934639690.1585258051950.0142711761218-0.05282799465090.56221493167-0.0580610244450.34075130351-3.58579604839-23.05902480413.75376300202
23.35210089752-0.3197154571760.7534988873570.198509189823-0.1117757329560.719855614507-0.3123130990170.2246882658690.5223614597430.05326400779210.0123414068917-0.0853111443192-0.1759108492910.143233023003-0.08760923851470.1125249578240.0707355698782-0.03418625500380.544948222162-0.01173553816680.307761316897-6.58853862652-21.4518495632-1.05269963835
32.93807208681.68192510842-0.5865456828921.08437903026-0.3446540820041.19101756353-0.1335135834480.1743173678560.117550603875-0.0863398603147-0.100670267343-0.00963793375-0.1170863974180.329922867816-0.3937117931370.0851410844003-0.0239190854026-0.05529341436990.5424407464750.01588433383980.208273064584-2.00442620534-25.3781158035-6.05361660446
40.9987726499550.3984625929621.122270861991.20607326268-0.9537798424753.1318725763-0.191942950534-0.3208521203980.8553849851030.2022877837760.223721649721-0.7020681030580.0415806862840.5294704728890.004739784431110.168206815082-0.0400677527983-0.03670332611260.475392331195-0.07880181204690.4256493611495.34070514296-23.97541850924.89477584638
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 20 through 53 )20 - 5315 - 48
22chain 'A' and (resid 54 through 78 )54 - 7849 - 73
33chain 'A' and (resid 79 through 89 )79 - 8974 - 84
44chain 'A' and (resid 6 through 19 )6 - 191 - 14

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