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- PDB-10xh: Bifidobacterium bifidum DnaA DI -

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Basic information

Entry
Database: PDB / ID: 10xh
TitleBifidobacterium bifidum 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
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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


Theoretical massNumber of molelcules
Total (without water)20,2012
Polymers20,2012
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.931, 50.965, 47.724
Angle α, β, γ (deg.)90.000, 120.120, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 7 through 16 or resid 18...
d_2ens_1(chain "B" and (resid 7 through 16 or resid 18...

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_11GLYGLYTRPTRPAA7 - 1610 - 19
d_12ASPASPTHRTHRAA18 - 1921 - 22
d_13ARGARGLEULEUAA21 - 2324 - 26
d_14GLNGLNPROPROAA25 - 3128 - 34
d_15ASPASPLEULEUAA33 - 5236 - 55
d_16VALVALLEULEUAA54 - 7557 - 78
d_17ILEILEILEILEAA7780
d_18SERSERVALVALAA79 - 9082 - 93
d_21GLYGLYTRPTRPBB7 - 1610 - 19
d_22ASPASPTHRTHRBB18 - 1921 - 22
d_23ARGARGLEULEUBB21 - 2324 - 26
d_24GLNGLNPROPROBB25 - 3128 - 34
d_25ASPASPLEULEUBB33 - 5236 - 55
d_26VALVALLEULEUBB54 - 7557 - 78
d_27ILEILEILEILEBB7780
d_28SERSERVALVALBB79 - 9082 - 93

NCS oper: (Code: givenMatrix: (0.542487517227, 0.0421830569703, 0.83900410211), (0.0324214425571, -0.999045710545, 0.02926633396), (0.839437992776, 0.0113251024535, -0.543337462669)Vector: -2. ...NCS oper: (Code: given
Matrix: (0.542487517227, 0.0421830569703, 0.83900410211), (0.0324214425571, -0.999045710545, 0.02926633396), (0.839437992776, 0.0113251024535, -0.543337462669)
Vector: -2.83598820566, -3.73720008158, 5.19961061957)

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10100.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Gene: dnaA, GBA83_04370 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M5KVR3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) 1,4-butanediol; 100 mM sodium acetate/acetic acid, pH 4.5

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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: Jun 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→23.67 Å / Num. obs: 12871 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 1 / Rpim(I) all: 0.011 / Rrim(I) all: 0.043 / Net I/σ(I): 40.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 6 / Num. unique obs: 895 / CC1/2: 0.976 / Rpim(I) all: 0.122 / Rrim(I) all: 0.482 / % 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: 1.9→23.67 Å / SU ML: 0.2139 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 1282 9.99 %
Rwork0.1822 11555 -
obs0.1862 12837 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 0 110 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721401
X-RAY DIFFRACTIONf_angle_d0.87941920
X-RAY DIFFRACTIONf_chiral_restr0.0548231
X-RAY DIFFRACTIONf_plane_restr0.0059248
X-RAY DIFFRACTIONf_dihedral_angle_d12.3937527
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.72586096475 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.3131390.26691283X-RAY DIFFRACTION99.72
1.98-2.070.33021370.21131261X-RAY DIFFRACTION100
2.07-2.170.26191400.20391293X-RAY DIFFRACTION100
2.18-2.310.25071460.20141291X-RAY DIFFRACTION99.86
2.31-2.490.23361390.19841265X-RAY DIFFRACTION99.86
2.49-2.740.2681470.20881273X-RAY DIFFRACTION99.37
2.74-3.130.2241450.20391281X-RAY DIFFRACTION99.37
3.14-3.950.21331410.16091293X-RAY DIFFRACTION99.86
3.95-23.670.17091480.15181315X-RAY DIFFRACTION99.66
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)
17.160335871767.32276008019-0.7749743696318.7974850526-0.2311509403215.71428079-0.158676834592-1.973136004371.581928704330.7453748191440.7264546668391.545392847520.159159564434-1.3186016318-0.1409773498660.2445046764680.111189326413-0.02050266665310.910688252804-0.06279792495020.481446323693-3.2207704619611.84067043633.51792209413
26.090352947531.538700210481.976006911618.402583027683.574799545384.934295159930.1553083394240.2726540939510.2251652659090.1853263919340.1390808773710.0079665260655-0.2816015521280.0568229103062-0.1560930285670.12282294550.02418565503970.032700210790.2056713648310.001512335332560.1988657014539.082839785915.444522622815.1460862446
31.50759606335-0.471859204526-0.5094799894936.205901059251.383682113174.621496206870.0376162877804-0.497756797650.585125149863-0.16803816533-0.336593718347-0.298693198386-0.4230547018870.1918579533120.366757494960.132475391232-0.01941468101790.003503436491930.333859720562-0.09188396986720.31328822934316.61525734111.234116291813.844467127
48.50541629094-0.569578958657-1.276193087145.50660353190.8923272651046.66631481497-0.268376931174-0.619471116779-0.1732582430930.466499279760.0515371015341-0.4784241596670.2082314009750.6994049215020.2445144900450.1606988466520.0369457907029-0.02940556101780.23182975303-0.01979792789470.24262885727617.07076705354.7620917960515.9121096409
52.17557105981-3.4203587218-2.030713353567.009856625660.6230852750738.51076278724-0.234822832608-0.402002985613-0.3510784777850.9675812895020.2733139253510.6419768863620.0313755747879-0.196379788509-0.04804826989460.2442123042170.0154092845980.1032168988640.210859549441-0.03621644169150.2349734595786.139525071919.4578742724620.6005013054
67.03086674101-4.28797318091-1.238930909555.946495312712.351230767557.453011906090.1833604288560.1622046349580.4936805883150.1258160799770.05424633731060.2222000429170.160199669409-0.131543213325-0.2988121807640.142411764546-0.04151340725640.03211919640520.1142873607710.01001258734710.19896395987310.40662712452.8359344422713.9260041548
74.49113067394-5.90303796477-3.091067257148.480133206143.804555043694.29756340294-0.3127541730880.353120956634-1.03655668028-0.00104028688779-0.03843379351750.4562281209350.881472568395-0.0161941424860.428725664370.705231206798-0.09667700658070.1271221548710.283746768994-0.065067323370.41620117187715.0073850848-18.26936209674.46208926445
87.96206035921-7.39540404608-5.019010576448.769384651715.637380601858.12265761226-1.12104935177-1.02203475104-0.6552843845730.9851254263540.419475571410.954018696310.5587132746140.4189655420910.3208176997240.7390552978910.253103018450.1364109670920.54004397226-0.04318170805560.53268359409125.0008612168-17.861013822512.9291814607
92.6961840979-0.509701540256-0.7458395759699.49251825386-5.314145119746.811688457-0.3331251910230.265636401279-0.415438421238-0.2172720558650.002133563405080.1034578021330.771691348255-0.1841954066580.3763483496190.36822950281-0.09812159733210.1589902270980.210910697755-0.04295151720620.2486062176879.5349442345-9.48491112610.564077309
109.06873174988-1.176141291171.056647625035.017054749340.4185179384812.75445586815-0.661731146546-0.0979473185379-0.5257188562730.1471045347250.4011629073-0.4615904141810.4115277190750.4167030717530.2722500621380.3345873993190.04034601607160.1271808145860.248928957069-0.008973525459050.2348973794319.8480632965-7.3362865566611.3648885351
117.71805277356-3.511030101011.887299520022.13303012559-2.023199770324.318332123710.2963648725221.12704800192-0.663521085319-0.810414401365-0.214882611024-0.2533856318290.8854846843410.353199363983-0.04350967063390.601536913763-0.07900987350570.1588882572820.371914064776-0.1043004249910.32639263716818.4241333665-11.767563581-1.27819543084
127.59217455197-0.548401517081-2.442515726335.913058873462.193312375561.47772417073-0.4674971017220.310273620435-0.283502050281-0.5568609091730.413494494782-0.04353946978590.3190291957370.0391025014193-0.05938782823030.327422966698-0.06511308849780.1294226530740.17683808397-0.01372028792320.2493677285714.8462579932-5.652121643116.45929046642
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 7 )AA1 - 71 - 7
22chain 'A' and (resid 8 through 30 )AA8 - 308 - 30
33chain 'A' and (resid 31 through 46 )AA31 - 4631 - 46
44chain 'A' and (resid 47 through 67 )AA47 - 6747 - 67
55chain 'A' and (resid 68 through 79 )AA68 - 7968 - 79
66chain 'A' and (resid 80 through 90 )AA80 - 9080 - 90
77chain 'B' and (resid 7 through 30 )BB7 - 302 - 25
88chain 'B' and (resid 31 through 38 )BB31 - 3826 - 33
99chain 'B' and (resid 39 through 46 )BB39 - 4634 - 41
1010chain 'B' and (resid 47 through 67 )BB47 - 6742 - 62
1111chain 'B' and (resid 68 through 79 )BB68 - 7963 - 74
1212chain 'B' and (resid 80 through 90 )BB80 - 9075 - 85

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