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- PDB-10xb: Nocardia asteroides DnaA DI protein in the I23 space group -

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Basic information

Entry
Database: PDB / ID: 10xb
TitleNocardia asteroides DnaA DI protein in the I23 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
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
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesNocardia asteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)10,8575
Polymers10,4891
Non-polymers3684
Water21612
1
A: Chromosomal replication initiator protein DnaA
hetero molecules

A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,71510
Polymers20,9782
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
Unit cell
Length a, b, c (Å)100.718, 100.718, 100.718
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

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10488.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia asteroides (bacteria) / Gene: dnaA, NCAST_27_00250 / Production host: Escherichia coli (E. coli) / References: UniProt: U5EFM3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.7 M Ammonium citrate tribasic dihydrate; 0.1 M Tris, pH 8.5

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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 PILATUS3 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: 2.4→35.61 Å / Num. obs: 6797 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 63.69 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 19 % / Mean I/σ(I) obs: 2 / Num. unique obs: 697 / CC1/2: 0.699 / Rpim(I) all: 0.327 / Rrim(I) all: 1.428 / % 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: 2.4→35.61 Å / SU ML: 0.1546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.5674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 341 5.03 %
Rwork0.2132 6432 -
obs0.2148 6773 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 24 12 756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032751
X-RAY DIFFRACTIONf_angle_d0.56071019
X-RAY DIFFRACTIONf_chiral_restr0.0431122
X-RAY DIFFRACTIONf_plane_restr0.0052131
X-RAY DIFFRACTIONf_dihedral_angle_d11.7496275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.030.32671660.34343176X-RAY DIFFRACTION99.94
3.03-35.610.22751750.18563256X-RAY DIFFRACTION99.56
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)
10.2372349864390.342684593844-0.7983422959643.1253236211-2.523894794333.40590552156-0.691096834759-1.01265029622-0.5125252211521.166510858190.5456167960220.09728678164750.208530383333-0.243278891076-0.6482960291511.89418884553-0.198582268352-0.2404484850841.312951555210.7913353887130.6485786545230.180700560562-43.1520870855-43.0971709471
26.013003707020.753038819453.20752820163.85121021076-1.564551278399.26862100308-0.24306390822-1.64654647955-0.4261506849831.423708303160.100154488616-0.346782706552-0.718382796571-1.187379045540.1022252593130.6926526134530.1585346587070.01450998177160.8411031609390.1973094540250.742648624439-7.93584307646-24.2178009638-34.7485727619
33.52874471931-3.88519014863-0.7902055213885.12393165782-1.721985607828.363705085430.102698773809-0.233580246253-1.416687352810.1974163822410.0959973143690.6430220337340.67695206763-0.250548897289-0.2241114046760.2679914075760.0414229772088-0.08450433544870.2707047068770.07808172598960.867081971887-6.41962662946-29.3784145163-46.8671857206
47.26942804039-5.693059585085.496741679894.51431694322-4.455368929784.63396371512-0.8650717374220.1065180333011.185123859460.150808003590.195771433661-0.934943763593-1.52682379060.9164860094980.8233717392170.607615869208-0.036011705373-0.1317377734440.4232328515760.007287529004150.723311166615-4.97862449522-16.7729851947-47.1000888051
58.51076529693-6.835200745924.931755660539.50280231672-5.423830801515.57205942063-0.440905011847-0.788514759321-0.152589100120.615148872213-0.074962270319-0.7006772778440.1245196787360.8905322619160.5251945506350.7377703217840.076143747297-0.08316206381940.7412038665670.3105010376250.613740765221.45142092769-27.8079055545-36.6276500265
62.7597636628-0.260040579188-2.00861555059.14468717346-0.6693620679328.311945376420.884586760985-0.14808907404-1.54902567421-0.409554179663-0.4088048527340.8404665971440.812977178141-0.540186756143-0.5374456075850.656496067342-0.0811816928378-0.1227772095110.214111192440.02477932387060.746658970826-6.68018390748-27.0579600341-49.5373161725
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 3 )-2 - 31 - 6
22chain 'A' and (resid 4 through 40 )4 - 407 - 43
33chain 'A' and (resid 41 through 58 )41 - 5844 - 61
44chain 'A' and (resid 59 through 69 )59 - 6962 - 72
55chain 'A' and (resid 70 through 84 )70 - 8473 - 87
66chain 'A' and (resid 85 through 96 )85 - 9688 - 99

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