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- PDB-10xp: Streptomyces lividans DnaA DI protein in the I222 space group. -

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Basic information

Entry
Database: PDB / ID: 10xp
TitleStreptomyces lividans DnaA DI protein in the I222 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
B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2715
Polymers20,1292
Non-polymers1423
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.739, 56.347, 153.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-101-

NA

21B-228-

HOH

31B-244-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10064.500 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2% (w/v) PEG 400; 100 mM Tris base/hydrochloric acid, pH 8.5; 2M 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: Aug 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.44 Å / Num. obs: 11469 / % possible obs: 99.8 % / Redundancy: 18.5 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.066 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 6.8 / Num. unique obs: 827 / CC1/2: 0.989 / Rpim(I) all: 0.084 / Rrim(I) all: 0.372 / % 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→20.44 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 1101 10 %
Rwork0.211 9904 -
obs0.216 11005 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.38 Å2
Refinement stepCycle: LAST / Resolution: 2→20.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 7 94 1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161362
X-RAY DIFFRACTIONf_angle_d0.49591861
X-RAY DIFFRACTIONf_chiral_restr0.0422218
X-RAY DIFFRACTIONf_plane_restr0.0054248
X-RAY DIFFRACTIONf_dihedral_angle_d15.6418507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.3521360.30831215X-RAY DIFFRACTION96.36
2.09-2.20.35081330.26821208X-RAY DIFFRACTION95.79
2.2-2.340.33811330.25621196X-RAY DIFFRACTION93.59
2.34-2.520.31031300.26681172X-RAY DIFFRACTION92.47
2.52-2.770.3041350.26911210X-RAY DIFFRACTION94.12
2.77-3.170.28231370.23671236X-RAY DIFFRACTION95.95
3.17-3.990.25161440.18781293X-RAY DIFFRACTION98.22
3.99-20.440.19771530.1631374X-RAY DIFFRACTION99.67
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)
13.65325869248-0.6260712841242.752541572455.429839918972.0479552324.86807273436-0.121769245162-1.342419819670.4283723250560.979907488765-0.596229290236-0.2246700679990.631979860875-0.5567532657680.546152122550.263289551807-0.03289472156470.03232409748410.452576774407-0.07270125512930.401559487265-15.6715628824-12.4094754812-22.2228501894
25.796165935180.05947741045421.547455815363.830933716990.4314028016846.841612024190.1321026153240.09114632284340.717963081041-0.0198715117239-0.06747827708340.17559204841-0.756117075061-0.485759576541-0.1355256089580.237301577695-0.01653251694830.0489535859730.2699229035130.007482379227490.326659582294-20.0993561817-13.929489018-29.8588130734
38.86915019348-0.05797407452954.080601848664.72533359769-0.03589939237194.339268611120.3221773857550.277909020556-0.02844305102980.0273264138329-0.1223903898870.07630156127490.1234972977720.0481161084897-0.2081850855490.2004300660070.03425997547460.06022707689960.202850779024-0.05884332604770.206847490791-16.9440790381-19.4546591467-32.0184973198
44.69759431146-0.1319530895911.42444448698.954038741531.317747452881.19537993112-0.0736123288304-0.2449374718660.201547655415-0.1976750998830.0933487336167-0.307556574836-0.8488955396871.277777557850.155826162630.277033803728-0.08758775379880.04202104488790.4170011654430.01562931994530.247991818077-29.8550977781-1.60768806387-9.72394596065
56.25167164954.558884084824.439536283213.387412659543.066332031083.58056582581-1.14467367321.85847546389-0.621475168061-0.9667815916390.954952396034-1.00022398535-0.3812933279561.665376405840.7129034349790.6997517839210.06509851110930.01591238420890.9120737076920.05749556419570.628458185675-28.6987014376-4.94173101519-24.2316703014
63.38249806098-0.3171895281360.6278265359772.234896840840.7047315843487.452927527230.0546523166619-0.0662698561113-0.268206490384-0.252269680008-0.0769582231627-0.1326064662361.142993707170.4893164643460.02057310989250.5084999224880.04910998766910.01985778087660.3044667198610.01678404257730.226140588624-34.9955526695-10.7376565801-13.1296187788
72.947933069172.13880612432-0.1223886125578.06294056775-0.686757278974.912906021530.811735249475-1.48723731881-0.9547280808920.0472569465912-0.498064862378-0.4049529072661.025506455220.691811563925-0.3251563674970.4234524811310.0410381791322-0.0180035011350.3948259441580.03536399722640.154156216889-33.4609618323-12.856608219-6.30877902762
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 22 )AA9 - 221 - 14
22chain 'A' and (resid 23 through 56 )AA23 - 5615 - 48
33chain 'A' and (resid 57 through 93 )AA57 - 9349 - 85
44chain 'B' and (resid 6 through 23 )BB6 - 231 - 18
55chain 'B' and (resid 24 through 32 )BB24 - 3219 - 27
66chain 'B' and (resid 33 through 81 )BB33 - 8128 - 76
77chain 'B' and (resid 82 through 93 )BB82 - 9377 - 88

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