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- PDB-8jmk: Structure of Helicobacter pylori Soj mutant, D41A bound to DNA -

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Basic information

Entry
Database: PDB / ID: 8jmk
TitleStructure of Helicobacter pylori Soj mutant, D41A bound to DNA
Components
  • DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
  • SpoOJ regulator (Soj)
KeywordsDNA BINDING PROTEIN / Helicobacter pylori / chromosome partition
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / SpoOJ regulator (Soj)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, C.T. / Chu, C.H. / Sun, Y.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB.
Authors: Chu, C.H. / Wu, C.T. / Lin, M.G. / Yen, C.Y. / Wu, Y.Z. / Hsiao, C.D. / Sun, Y.J.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SpoOJ regulator (Soj)
B: SpoOJ regulator (Soj)
C: SpoOJ regulator (Soj)
D: SpoOJ regulator (Soj)
E: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
F: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,50214
Polymers131,3766
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-123 kcal/mol
Surface area46870 Å2
Unit cell
Length a, b, c (Å)75.200, 75.198, 81.124
Angle α, β, γ (deg.)71.25, 71.38, 67.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SpoOJ regulator (Soj)


Mass: 29158.982 Da / Num. of mol.: 4 / Mutation: D41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1139 / Production host: Escherichia coli (E. coli) / References: UniProt: O25759
#2: DNA chain DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')


Mass: 7256.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')


Mass: 7483.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 25% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 44627 / % possible obs: 96.4 % / Redundancy: 1.9 % / CC1/2: 0.756 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.691.90.33744660.7560.9280.3370.4770.85596.6
2.69-2.81.90.23744440.8660.9640.2370.3360.88196.8
2.8-2.931.90.244740.8810.9680.20.2820.86496.8
2.93-3.081.90.14844820.9350.9830.1480.2090.91496.8
3.08-3.281.90.10144990.9650.9910.1010.1420.9897
3.28-3.5320.06244630.9860.9960.0620.0871.05296
3.53-3.8820.04244600.9910.9980.0420.060.98296.4
3.88-4.4420.03144380.9940.9990.0310.0440.90195
4.44-5.5920.02543960.9960.9990.0250.0360.83795.3
5.59-301.90.02145050.99810.0210.030.86797.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUC

6iuc


Resolution: 2.7→27.879 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3034 1882 4.76 %
Rwork0.2238 --
obs0.2276 39518 47.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→27.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 984 128 0 9312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019586
X-RAY DIFFRACTIONf_angle_d1.61913192
X-RAY DIFFRACTIONf_dihedral_angle_d21.3913666
X-RAY DIFFRACTIONf_chiral_restr0.111532
X-RAY DIFFRACTIONf_plane_restr0.0071476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77290.3871270.29292508X-RAY DIFFRACTION41
2.7729-2.85450.37941410.26932817X-RAY DIFFRACTION47
2.8545-2.94650.33351500.26262941X-RAY DIFFRACTION48
2.9465-3.05170.35341440.25122990X-RAY DIFFRACTION48
3.0517-3.17370.35761480.25672949X-RAY DIFFRACTION49
3.1737-3.31790.29591440.23962942X-RAY DIFFRACTION48
3.3179-3.49250.33891470.24522920X-RAY DIFFRACTION48
3.4925-3.71090.32481420.22972931X-RAY DIFFRACTION48
3.7109-3.99670.33291450.22652956X-RAY DIFFRACTION48
3.9967-4.39740.29341490.20472898X-RAY DIFFRACTION48
4.3974-5.03050.24361460.18762874X-RAY DIFFRACTION47
5.0305-6.32570.28911500.21492944X-RAY DIFFRACTION48
6.3257-27.8790.22991490.18932966X-RAY DIFFRACTION49
Refinement TLS params.Method: refined / Origin x: 35.0209 Å / Origin y: -31.7739 Å / Origin z: 70.5936 Å
111213212223313233
T0.2189 Å20.0695 Å2-0.0505 Å2-0.1537 Å2-0.0414 Å2--0.2411 Å2
L1.1877 °20.5559 °2-0.7333 °2-0.7169 °2-0.497 °2--1.3255 °2
S-0.0424 Å °-0.0063 Å °0.0108 Å °-0.0076 Å °-0.024 Å °0.0014 Å °0.0215 Å °-0.0169 Å °0.0536 Å °
Refinement TLS groupSelection details: all

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