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- PDB-10wy: Rhodococcus hoagii DnaA DI in the P4(3)2(1)2 space group -

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Basic information

Entry
Database: PDB / ID: 10wy
TitleRhodococcus hoagii DnaA DI in the P4(3)2(1)2 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 speciesPrescottella equi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Nucleic Acids Res. / Year: 2026
Title: Structures of DnaA domain I reveal a dimer conserved across Actinomycetes.
Authors: Ellis, P.K. / Srinivasu, B.Y. / Chavez Orozco Jr., J. / Wray, G.A. / Wales, T.E. / Schumacher, M.A.
History
DepositionFeb 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 1, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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
B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7935
Polymers28,6002
Non-polymers1943
Water2,594144
1
B: Chromosomal replication initiator protein DnaA
hetero molecules

A: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7935
Polymers28,6002
Non-polymers1943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
Buried area1400 Å2
ΔGint-33 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.646, 60.646, 132.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 14299.858 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prescottella equi (bacteria)
Gene: dnaA, A5N68_15520, GS453_12660, GS505_04630, GS551_08815, GS882_16585, GS947_16945
Production host: Escherichia coli (E. coli) / References: UniProt: A0A9Q2ULC7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.2 M Ammonium Sulfate, 0.2 M Lithium Sulfate, 0.1 M Tris, pH 8.33.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.6→44.73 Å / Num. obs: 33536 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.055 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1608 / CC1/2: 0.921 / Rpim(I) all: 0.188 / Rrim(I) all: 0.496 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.73 Å / SU ML: 0.1594 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.8847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 1673 5 %
Rwork0.1745 31785 -
obs0.1757 33458 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 10 144 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371431
X-RAY DIFFRACTIONf_angle_d0.73061957
X-RAY DIFFRACTIONf_chiral_restr0.0443231
X-RAY DIFFRACTIONf_plane_restr0.0104254
X-RAY DIFFRACTIONf_dihedral_angle_d15.2096544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.23851360.24192578X-RAY DIFFRACTION99.63
1.65-1.70.21831350.20272586X-RAY DIFFRACTION99.89
1.7-1.760.21751370.19262606X-RAY DIFFRACTION100
1.76-1.830.21721380.1922606X-RAY DIFFRACTION100
1.83-1.910.29321360.23022603X-RAY DIFFRACTION99.93
1.91-2.020.22851380.19142622X-RAY DIFFRACTION99.96
2.02-2.140.18511390.16912628X-RAY DIFFRACTION100
2.14-2.310.18561390.172634X-RAY DIFFRACTION99.89
2.31-2.540.16921380.16752654X-RAY DIFFRACTION100
2.54-2.910.19581420.17162679X-RAY DIFFRACTION99.96
2.91-3.660.21851430.17192705X-RAY DIFFRACTION99.89
3.66-44.730.18041520.16542884X-RAY DIFFRACTION99.93
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)
12.19646517445-0.7778763257381.201673647381.514271635370.3189452956882.241560603640.0386962476597-0.225051423436-0.1020627820520.07007160842440.0836604878461-0.1974908716620.04633739249160.480592986269-0.02409213903290.2557592180050.0132127508183-0.09119119213360.269289273826-0.01859234528550.2806857460650.646178162063-24.040265092-4.66015260377
26.66235161801-5.3810016499-7.120977824285.229825532496.930947396849.536029133220.0584627230825-1.017751493480.1189074754780.4600552578570.489837162258-0.8332785859130.06530377237350.52231932195-0.5768277024550.3398581654130.0515933136394-0.05691299129290.375716978697-0.03044738235450.311040229719-13.049295402-19.21013009034.5779565061
37.21482184243-5.15962510403-3.039660416266.208302610165.181223638284.94246804096-0.0509547988645-0.161751015965-0.1794802036560.1482155483870.157452285737-0.08293291065960.474995720887-0.0106963999063-0.06629267126270.335815300912-0.0492249533885-0.02967747975090.171583514849-0.001949782735570.232716551336-12.9375620313-27.7463532965-5.57204398959
47.028145928843.26248846418-4.544535067493.73708648905-3.747829206744.4219402314-0.143219182219-0.0236627254038-0.520417296103-0.217076858751-0.089431584586-0.5669049581040.6802652772290.5008941156290.3270527975230.187421728340.0392388931934-0.02916349672720.270009874115-0.006586283626460.3448266220830.339401693341-24.478540429-14.6579747319
56.647985488163.61953445001-0.210263151857.79323914767-0.6782934904683.96323536935-0.0265884344504-0.0134114948826-0.149246497736-0.02078730692740.03292987053170.2032836749940.0435837992001-0.1551951854520.002875619827990.1873906028090.0131336596709-0.05676484289470.14334175113-0.0003904606649010.169904480472-10.1576375154-21.1316927763-14.6077775014
62.86837439903-0.1249427272454.27666650393.55370060436-2.057404026318.73069682934-0.0964818797423-0.3546511941040.3273178500350.395985732069-0.0382229388836-0.346576032795-0.4661968092980.181753979910.1525956762430.262296536067-0.00771643331708-0.05893668810610.207688330737-0.05279719362610.255180871213-2.88949997873-14.6210657032-5.26737039393
76.358882935966.126048658995.562514186576.170112995925.314934018155.958995788550.09039737537790.469448271745-0.3852313999030.263375598470.290261887956-0.9890078867920.2382260970950.643548148191-0.2797014128330.309920056402-0.00209019454942-0.07027468864180.25172664951-0.005038833710550.363725697719-2.86622007064-17.8145426699-14.9875722443
82.89527507603-2.730623536524.65515812098.6883454777-2.34613370119.33028890374-0.4042589773280.51584691040.946928225854-0.7770249790380.140536433157-0.437692433776-0.7139720884850.6449668086430.2151597691550.455456031463-0.0673978895080.03944226168030.245434693553-0.01671854511030.249981668823-7.23947489242-10.285647759-35.6165565039
96.57065633138-1.55333773769-6.929392368977.20165795678-4.101491106831.99861676919-0.7664010403973.36854225073-1.5461907081-2.17390503291-1.293087000351.30227635572.62161512746-0.6132096878151.227883520770.8267780998630.131920044-0.1916144567070.934121534478-0.2191423217220.730958051671-21.9666714493-12.9881449518-37.1040748883
109.64230170765-4.419259838790.8964209005575.74654277618-0.5490633711444.08317103246-0.0860416756720.309743316310.011075843619-0.2956136004070.0744739310046-0.0270422718688-0.3158602085540.2823351383190.05919715457890.305707387469-0.0140770877443-0.00758005799750.153525429091-0.02881689625740.23165193165-11.1788604884-8.00765023434-27.5355736213
117.85682529925-2.53010517776-2.230914375767.740578584182.754783760666.43488997529-0.0462948823530.0346166461530.02836438842910.2447678729860.06498314109360.288616161286-0.0194512861584-0.0660450156525-0.02132579051950.209101529281-0.000533909575071-0.04328752272930.09868291860760.01983313573050.10455949758-11.1792328282-11.8799498236-21.0647048114
122.59018401093-2.83213663462-2.338302998036.78482102953.2070178125.03140947539-0.05497449458120.150681379243-0.148515052468-0.2293271951640.0525643204001-0.07106986976360.1480396505130.00674618687218-0.01223243925530.239399590072-0.01708647413790.009548110140690.162572827154-0.009783365637440.2029305872-8.39117537535-18.0691878368-28.9352841582
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 20 )AA5 - 202 - 17
22chain 'A' and (resid 21 through 30 )AA21 - 3018 - 27
33chain 'A' and (resid 31 through 39 )AA31 - 3928 - 36
44chain 'A' and (resid 40 through 46 )AA40 - 4637 - 43
55chain 'A' and (resid 47 through 67 )AA47 - 6744 - 64
66chain 'A' and (resid 68 through 79 )AA68 - 7965 - 76
77chain 'A' and (resid 80 through 91 )AA80 - 9177 - 88
88chain 'B' and (resid 6 through 20 )BB6 - 204 - 18
99chain 'B' and (resid 21 through 30 )BB21 - 3019 - 28
1010chain 'B' and (resid 31 through 46 )BB31 - 4629 - 44
1111chain 'B' and (resid 47 through 67 )BB47 - 6745 - 65
1212chain 'B' and (resid 68 through 91 )BB68 - 9166 - 89

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