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Open data
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Basic information
Entry | Database: PDB / ID: 5u1g | ||||||
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Title | Structure of TP228 ParA-AMPPNP-ParB complex | ||||||
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![]() | CELL CYCLE / REPLICATION / DNA segregation / Walker-box / partition | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | unidentified plasmid (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schumacher, M.A. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.3 KB | Display | ![]() |
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PDB format | ![]() | 140.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u1jC ![]() 4e07S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23062.365 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified plasmid (others) / Production host: ![]() ![]() #2: Protein/peptide | Mass: 2253.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified plasmid (others) / Production host: ![]() ![]() #3: Chemical | ChemComp-ANP / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage 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 parameters | Biso max: 115.8 Å2 / Biso mean: 56.84 Å2 / Biso min: 6.55 Å2
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Refinement step | Cycle: final / Resolution: 3.64→73.268 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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