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- PDB-8ray: ParA in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 8ray
TitleParA in complex with ATP
ComponentsParA family protein
KeywordsREPLICATION / Soj / DNA replication
Function / homology
Function and homology information


chromosome segregation / DNA binding / ATP binding / cytoplasm
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chromosome partitioning protein ParA
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMais, C.-N. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Cell / Year: 2025
Title: Molecular basis of ParA ATPase activation by the CTPase ParB during bacterial chromosome segregation
Authors: Schnabel, L. / Osorio-Valeriano, M. / Perez-Borrajero, C. / Steinchen, W. / Mais, C.-N. / Simon, B. / Hanssmann, J. / Thamm, M. / Hennig, J. / Bange, G. / Thanbichler, M.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ParA family protein
A: ParA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1366
Polymers56,0732
Non-polymers1,0634
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-39 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.740, 85.780, 97.280
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 ParA family protein


Mass: 28036.293 Da / Num. of mol.: 2 / Mutation: D60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: MXAN_7477 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1CVJ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10% glycerol, 0.1M MES, 30% PEG-600, 5% PEG-1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.58→37.72 Å / Num. obs: 67745 / % possible obs: 98.32 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1363 / Net I/σ(I): 12.99
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 2.179 / Num. unique obs: 5683 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→37.72 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 3383 5 %0.05
Rwork0.1736 ---
obs0.1749 67709 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3905 0 64 383 4352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164029
X-RAY DIFFRACTIONf_angle_d1.5915481
X-RAY DIFFRACTIONf_dihedral_angle_d18.921585
X-RAY DIFFRACTIONf_chiral_restr0.084646
X-RAY DIFFRACTIONf_plane_restr0.009702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.387870.35831664X-RAY DIFFRACTION61
1.61-1.630.30611400.30942647X-RAY DIFFRACTION100
1.63-1.650.29591410.27572704X-RAY DIFFRACTION100
1.65-1.680.30671430.24912702X-RAY DIFFRACTION100
1.68-1.710.31011400.23572700X-RAY DIFFRACTION100
1.71-1.740.25131410.21382685X-RAY DIFFRACTION100
1.74-1.780.21561410.2022685X-RAY DIFFRACTION100
1.78-1.810.18951410.18712693X-RAY DIFFRACTION100
1.81-1.850.19251400.19092688X-RAY DIFFRACTION100
1.85-1.890.22431420.18662687X-RAY DIFFRACTION100
1.89-1.940.21291430.17682721X-RAY DIFFRACTION100
1.94-1.990.22891430.16732700X-RAY DIFFRACTION100
1.99-2.050.19431420.16232713X-RAY DIFFRACTION100
2.05-2.120.1881430.15722695X-RAY DIFFRACTION100
2.12-2.190.2361440.15942731X-RAY DIFFRACTION100
2.19-2.280.18121420.15532707X-RAY DIFFRACTION100
2.28-2.390.21371450.1712740X-RAY DIFFRACTION100
2.39-2.510.18151430.16252719X-RAY DIFFRACTION100
2.51-2.670.18781430.1642727X-RAY DIFFRACTION100
2.67-2.870.18941450.16632745X-RAY DIFFRACTION100
2.88-3.160.18151470.16742778X-RAY DIFFRACTION100
3.16-3.620.16891450.16532751X-RAY DIFFRACTION100
3.62-4.560.17591480.15362811X-RAY DIFFRACTION100
4.56-37.720.2061540.17832933X-RAY DIFFRACTION100

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