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Open data
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Basic information
Entry | Database: PDB / ID: 1bdv | ||||||
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Title | ARC FV10 COCRYSTAL | ||||||
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![]() | GENE REGULATION/DNA / GENE-REGULATING PROTEIN / GENE REGULATION-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schildbach, J.F. / Karzai, A.W. / Raumann, B.E. / Sauer, R.T. | ||||||
![]() | ![]() Title: Origins of DNA-binding specificity: role of protein contacts with the DNA backbone. Authors: Schildbach, J.F. / Karzai, A.W. / Raumann, B.E. / Sauer, R.T. #1: ![]() Title: DNA Recognition by Beta-Sheets in the Arc Repressor-Operator Crystal Structure Authors: Raumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.1 KB | Display | ![]() |
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Full document | ![]() | 404.6 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bazC ![]() 1bdtC ![]() 1parS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: DNA chain | Mass: 6756.387 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6743.404 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 6190.229 Da / Num. of mol.: 4 / Mutation: F10V 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: 2.37 Å3/Da / Density % sol: 48.02 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 8691 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 62 |
Reflection shell | *PLUS % possible obs: 62 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PAR Resolution: 2.8→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→20 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.252 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.252 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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