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- PDB-1f4k: CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f4k | ||||||
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Title | CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX | ||||||
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![]() | REPLICATION/DNA / winged-helix protein-DNA complex / REPLICATION AND TERMINATION / FORK ARREST MECHANISM / REPLICATION-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wilce, J.A. / Vivian, J.P. / Hastings, A.F. / Otting, G. / Folmer, R.H.A. / Duggin, I.G. / Wake, R.G. / Wilce, M.C.J. | ||||||
![]() | ![]() Title: Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest Authors: Wilce, J.A. / Vivian, J.P. / Hastings, A.F. / Otting, G. / Folmer, R.H. / Duggin, I.G. / Wake, R.G. / Wilce, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The whole biological assembly is contained in the asymmetric unit. It comprises a homodimer constructed from chain A and B bound to double stranded DNA (chains D and E). |
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Components
#1: DNA chain | Mass: 6445.209 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS | ||
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#2: DNA chain | Mass: 6436.195 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS | ||
#3: Protein | Mass: 14531.099 Da / Num. of mol.: 2 / Mutation: C110S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 5% PEG 4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 15166 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.175 / % possible all: 54.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 15166 / Num. measured all: 147110 |
Reflection shell | *PLUS % possible obs: 54.2 % |
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Processing
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Refinement | Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: protein_rep.param, dna-rna_rep.param, water_rep.param
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.232 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rfactor Rfree: 0.381 / Rfactor obs: 0.301 |