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- PDB-5u1g: Structure of TP228 ParA-AMPPNP-ParB complex -

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Basic information

Entry
Database: PDB / ID: 5u1g
TitleStructure of TP228 ParA-AMPPNP-ParB complex
Components
  • ParA
  • TP228 ParB fragment
KeywordsCELL CYCLE / REPLICATION / DNA segregation / Walker-box / partition
Function / homology
Function and homology information


DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / transcription repressor complex / protein-DNA complex / nucleic acid binding / negative regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
DNA partition complex, ParG / ParG / Arc-type ribbon-helix-helix / Ribbon-helix-helix / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Plasmid partition protein ParG
Similarity search - Component
Biological speciesunidentified plasmid (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.64 Å
AuthorsSchumacher, M.A.
CitationJournal: Genes Dev. / Year: 2017
Title: Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation.
Authors: Zhang, H. / Schumacher, M.A.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: ParA
A: ParA
B: ParA
C: ParA
Y: TP228 ParB fragment
Z: TP228 ParB fragment
K: TP228 ParB fragment
R: TP228 ParB fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,28912
Polymers101,2648
Non-polymers2,0254
Water00
1
D: ParA
C: ParA
Z: TP228 ParB fragment
K: TP228 ParB fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6446
Polymers50,6324
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-33 kcal/mol
Surface area17330 Å2
MethodPISA
2
A: ParA
B: ParA
Y: TP228 ParB fragment
R: TP228 ParB fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6446
Polymers50,6324
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-31 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.360, 87.510, 133.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ParA


Mass: 23062.365 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified plasmid (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide
TP228 ParB fragment


Mass: 2253.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified plasmid (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJ82*PLUS
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 20000, 0.1 M MgCl2, 0.1 M Tris pH 8.5. took 6 months to grow, Mass spec revealed TP228 FL ParB protein had degraded and only N-term region revealed in crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→87.36 Å / Biso Wilson estimate: 59.83 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.127 / Rsym value: 14.5
Reflection shellResolution: 3.64→3.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.843 / % possible all: 78.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40000000 / Resolution: 3.64→73.268 Å / FOM work R set: 0.7793 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 927 10.01 %
Rwork0.2517 8332 -
obs0.2528 9259 77.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 115.8 Å2 / Biso mean: 56.84 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1--20.557 Å2-0 Å20 Å2
2---13.1367 Å2-0 Å2
3---42.5789 Å2
Refinement stepCycle: final / Resolution: 3.64→73.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 124 0 6742
Biso mean--35.2 --
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126871
X-RAY DIFFRACTIONf_angle_d1.4879320
X-RAY DIFFRACTIONf_chiral_restr0.0891123
X-RAY DIFFRACTIONf_plane_restr0.0061155
X-RAY DIFFRACTIONf_dihedral_angle_d18.9182496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.64-3.83190.2991360.29291199133581
3.8319-4.0720.27461310.26151200133180
4.072-4.38630.25431320.26441228136080
4.3863-4.82770.19161320.22171187131978
4.8277-5.5260.29481360.26151189132577
5.526-6.96140.33751270.29271168129575
6.9614-73.28280.23751330.20971161129471

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