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- PDB-8jmj: Structure of Helicobacter pylori Soj-DNA-Spo0J complex -

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Basic information

Entry
Database: PDB / ID: 8jmj
TitleStructure of Helicobacter pylori Soj-DNA-Spo0J complex
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')
  • Probable chromosome-partitioning protein ParB
  • SpoOJ regulator (Soj)
KeywordsDNA BINDING PROTEIN / Helicobacter pylori / chromosome partition
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function
ParB/Spo0J, HTH domain / HTH domain found in ParB protein / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Probable chromosome-partitioning protein ParB / SpoOJ regulator (Soj)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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

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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')
L: Probable chromosome-partitioning protein ParB
K: Probable chromosome-partitioning protein ParB
M: Probable chromosome-partitioning protein ParB
N: Probable chromosome-partitioning protein ParB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,80818
Polymers135,68210
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.178, 75.193, 81.116
Angle α, β, γ (deg.)71.34, 71.46, 67.70
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 2 molecules EF

#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)

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Protein / Protein/peptide , 2 types, 8 molecules ABCDLKMN

#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
#4: Protein/peptide
Probable chromosome-partitioning protein ParB


Mass: 1076.337 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori 26695 (bacteria) / References: UniProt: O25758

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Non-polymers , 2 types, 8 molecules

#5: 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
#6: Chemical
ChemComp-MG / MAGNESIUM ION


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

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Details

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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M MES and 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: 2.57→30 Å / Num. obs: 46674 / % possible obs: 96.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.57-2.661.80.32146580.7780.9360.3210.4550.77596.2
2.66-2.771.90.23546940.8830.9680.2350.3320.81196.2
2.77-2.891.90.18946840.8990.9730.1890.2670.87396.5
2.89-3.051.90.14646820.9380.9840.1460.2070.86597.1
3.05-3.241.90.09846380.9670.9910.0980.1390.88796.7
3.24-3.491.90.05946770.9860.9970.0590.0840.95696.7
3.49-3.8420.0446450.9920.9980.040.0571.01696.6
3.84-4.3920.02846800.9960.9990.0280.040.87295.8
4.39-5.5320.02346050.9970.9990.0230.0330.86295.7
5.53-3020.0247110.99810.020.0280.83997.4

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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: 2.57→28.565 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3017 2007 4.58 %
Rwork0.224 --
obs0.2275 43830 90.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→28.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 984 128 0 9555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119825
X-RAY DIFFRACTIONf_angle_d1.77413497
X-RAY DIFFRACTIONf_dihedral_angle_d21.1333755
X-RAY DIFFRACTIONf_chiral_restr0.121564
X-RAY DIFFRACTIONf_plane_restr0.0071514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5704-2.63460.375800.2721682X-RAY DIFFRACTION51
2.6346-2.70580.39151060.28982328X-RAY DIFFRACTION69
2.7058-2.78540.42461400.26182921X-RAY DIFFRACTION89
2.7854-2.87520.36211540.25923139X-RAY DIFFRACTION96
2.8752-2.97780.37311550.26273162X-RAY DIFFRACTION97
2.9778-3.09690.29131530.2643194X-RAY DIFFRACTION97
3.0969-3.23770.35941490.25793190X-RAY DIFFRACTION97
3.2377-3.40810.31621530.23833203X-RAY DIFFRACTION97
3.4081-3.62130.28161530.22143177X-RAY DIFFRACTION97
3.6213-3.90020.31521520.22113153X-RAY DIFFRACTION96
3.9002-4.29150.26581500.20743148X-RAY DIFFRACTION96
4.2915-4.90980.27931480.18753122X-RAY DIFFRACTION95
4.9098-6.17550.27561550.22043217X-RAY DIFFRACTION97
6.1755-28.5650.2521590.19043187X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -21.6515 Å / Origin y: 89.6121 Å / Origin z: -51.9248 Å
111213212223313233
T0.1945 Å20.0734 Å2-0.0419 Å2-0.1352 Å2-0.0347 Å2--0.2302 Å2
L1.2582 °20.6146 °2-0.855 °2-0.7352 °2-0.6353 °2--1.5053 °2
S-0.0243 Å °-0.0075 Å °0.0187 Å °-0.0094 Å °-0.0252 Å °0.004 Å °0.0182 Å °0.0042 Å °0.0308 Å °
Refinement TLS groupSelection details: all

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