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- PDB-10wz: Rhodococcus hoagii DnaA DI in the P6(2)22 space group -

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Basic information

Entry
Database: PDB / ID: 10wz
TitleRhodococcus hoagii DnaA DI in the P6(2)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
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 / MOLECULAR REPLACEMENT / Resolution: 3 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
B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3652
Polymers14,3001
Non-polymers651
Water1448
1
B: Chromosomal replication initiator protein DnaA
hetero molecules

B: Chromosomal replication initiator protein DnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7314
Polymers28,6002
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area1450 Å2
ΔGint-63 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.100, 61.100, 132.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11B-201-

ZN

21B-305-

HOH

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Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 14299.858 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 1000, 100 mM Sodium acetate/acetic acid pH 4.5, 200 mM Zinc acetate

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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: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3→20.69 Å / Num. obs: 3312 / % possible obs: 99.7 % / Redundancy: 15.9 % / Biso Wilson estimate: 64.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.132 / Net I/σ(I): 16.2
Reflection shellResolution: 3→3.18 Å / Redundancy: 17.4 % / Mean I/σ(I) obs: 4 / Num. unique obs: 517 / CC1/2: 0.993 / Rpim(I) all: 0.114 / Rrim(I) all: 0.483 / % 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: 3→20.42 Å / SU ML: 0.3296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2607 162 4.99 %
Rwork0.218 3083 -
obs0.2201 3245 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.5 Å2
Refinement stepCycle: LAST / Resolution: 3→20.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 1 8 682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034684
X-RAY DIFFRACTIONf_angle_d0.693931
X-RAY DIFFRACTIONf_chiral_restr0.0422111
X-RAY DIFFRACTIONf_plane_restr0.0051120
X-RAY DIFFRACTIONf_dihedral_angle_d5.260195
LS refinement shellResolution: 3→3.42 Å
RfactorNum. reflection% reflection
Rfree0.2607 162 -
Rwork0.218 3083 -
obs--98.66 %
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)
12.590441414230.410393402379-1.089692865492.327135136134.053399078848.574637988870.796335355185-0.09506605272970.0872359508119-0.849852521144-0.3397536903870.423236814053-1.33356808816-0.20050873293-0.3659172652380.618776370992-0.133137469064-0.06107024233530.45195098280.06872993120350.504712620357-29.919366138925.0452431093-6.46269574988
24.25704172992-4.45162280514-4.94192041818.600720696157.723429029787.38700126375-0.212270539428-0.0156879581240.1995639901361.04484970026-0.7051918357810.1933607837460.97923389573-0.3584802699080.6974118284960.3970771179210.06193312869560.1070238998020.8561987798320.1387679577180.596581696153-19.648273045215.3127045802-0.648514899969
38.846563891150.1889048772684.776419582265.568968873840.8096127656037.09440785109-0.4261998647030.435252452233-0.281685360967-0.240614213570.113461683596-0.172565971634-1.440472504180.6234078393450.2560463811990.502874099007-0.1530053451580.08719771564140.4038700948820.001347590120540.354724061984-23.906237906624.1351616373-13.1691191675
47.980888481453.18821848612-1.759568338855.36388128867-0.1613561308521.36120400291-0.0614649664540.650083080396-0.694965528598-0.225529818203-0.0338737913663-0.2490739287840.0128115927150.2077980269850.2273151678990.67991285305-0.1678646191930.0439489091580.684930325547-0.1341872923480.266300027487-24.611727095719.4652615749-18.9508018452
58.987058432860.567108314706-4.64988168873.74182740095-3.702618639388.538386321130.04892727040470.380288518053-1.08640659093-0.465699550264-0.1949429720430.336887125182-0.528571358388-0.09536973384740.3157699919890.492863850462-0.05049968109380.0533360687530.504275349946-0.179340978540.287177705699-31.856598876417.2668223652-12.2458482579
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 6 through 20 )6 - 201 - 15
22chain 'B' and (resid 21 through 30 )21 - 3016 - 25
33chain 'B' and (resid 31 through 46 )31 - 4626 - 41
44chain 'B' and (resid 47 through 67 )47 - 6742 - 62
55chain 'B' and (resid 68 through 91 )68 - 9163 - 86

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