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- PDB-3fhw: Crystal structure of the protein priB from Bordetella parapertuss... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fhw | ||||||
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Title | Crystal structure of the protein priB from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR162. | ||||||
![]() | Primosomal replication protein n | ||||||
![]() | DNA BINDING PROTEIN / priB BpR162 X-RAY NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / DNA replication / DNA-binding / Primosome | ||||||
Function / homology | ![]() primosome complex / DNA replication, synthesis of primer / single-stranded DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the protein priB from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR162. Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 39.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | dimer |
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Components
#1: Protein | Mass: 12698.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 1.5M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 41038 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.3 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Authors explanation on why Rfree/R are high at this resolution: The analyses of the Patterson function reveals a significant off-origin peak that is 56.98 % of the origin peak, indicating ...Details: Authors explanation on why Rfree/R are high at this resolution: The analyses of the Patterson function reveals a significant off-origin peak that is 56.98 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 2.5284e-05. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.793 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→22.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 31.1109 Å / Origin y: 14.653 Å / Origin z: 18.9432 Å
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Refinement TLS group |
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