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- PDB-8jml: Structure of Helicobacter pylori Soj protein mutant, D41A -

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Basic information

Entry
Database: PDB / ID: 8jml
TitleStructure of Helicobacter pylori Soj protein mutant, D41A
ComponentsSpoOJ regulator (Soj)
KeywordsDNA BINDING PROTEIN / Helicobacter pylori / chromosome partition
Function / homology: / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / SpoOJ regulator (Soj)
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3816
Polymers58,3182
Non-polymers1,0634
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-43 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.137, 94.133, 111.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SpoOJ regulator (Soj)


Mass: 29158.982 Da / Num. of mol.: 2 / 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.1 M MgCl2, 14% PEG550MME, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 35035 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.863 / Rmerge(I) obs: 0.156 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.038.70.84817150.8630.9620.2980.9010.44899.9
2.03-2.079.80.76717370.8830.9680.2530.8080.47100
2.07-2.1110.90.72617000.9150.9780.2280.7620.477100
2.11-2.15120.7217150.940.9840.2150.7520.488100
2.15-2.212.70.69517470.9440.9860.20.7230.492100
2.2-2.2513.30.61817060.9390.9840.1740.6420.521100
2.25-2.3113.70.5817430.9650.9910.1610.6020.526100
2.31-2.37140.47417230.9740.9930.1310.4920.533100
2.37-2.4414.10.39917150.9810.9950.1090.4140.535100
2.44-2.5214.20.34517540.9850.9960.0940.3570.539100
2.52-2.6114.20.29517280.990.9970.0810.3060.56100
2.61-2.7114.20.23217430.9920.9980.0630.240.582100
2.71-2.8414.30.18517500.9940.9990.050.1920.627100
2.84-2.9914.40.16817400.9950.9990.0460.1740.688100
2.99-3.1714.40.13617570.9940.9990.0370.1410.784100
3.17-3.4214.50.10217650.9980.9990.0280.1060.902100
3.42-3.7614.30.08517710.9980.9990.0230.0880.954100
3.76-4.3114.30.06517890.99910.0180.0671.055100
4.31-5.42140.05518210.99910.0150.0570.992100
5.42-30130.0519160.99910.0140.0521.08100

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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: 6IUB

6iub


Resolution: 2→29.404 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1999 5.72 %
Rwork0.1711 --
obs0.174 34972 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 64 357 4513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094234
X-RAY DIFFRACTIONf_angle_d1.5495738
X-RAY DIFFRACTIONf_dihedral_angle_d15.571592
X-RAY DIFFRACTIONf_chiral_restr0.105669
X-RAY DIFFRACTIONf_plane_restr0.008713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04810.26571340.21272205X-RAY DIFFRACTION96
2.0481-2.10350.26891420.19262351X-RAY DIFFRACTION100
2.1035-2.16530.27321410.18772303X-RAY DIFFRACTION100
2.1653-2.23520.21931400.18182322X-RAY DIFFRACTION100
2.2352-2.31510.23111410.18112323X-RAY DIFFRACTION100
2.3151-2.40770.21541430.17552368X-RAY DIFFRACTION100
2.4077-2.51720.23571420.17892333X-RAY DIFFRACTION100
2.5172-2.64990.24751420.17512347X-RAY DIFFRACTION100
2.6499-2.81580.23321430.17522345X-RAY DIFFRACTION100
2.8158-3.0330.2311430.18622365X-RAY DIFFRACTION100
3.033-3.33780.2261430.18722356X-RAY DIFFRACTION100
3.3378-3.81990.21391440.15952392X-RAY DIFFRACTION100
3.8199-4.80930.20031480.14052431X-RAY DIFFRACTION100
4.8093-29.4040.18161530.16362532X-RAY DIFFRACTION100

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