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Open data
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Basic information
Entry | Database: PDB / ID: 1td3 | ||||||
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Title | Crystal structure of VSHP_BPP21 in space group C2 | ||||||
![]() | Head decoration protein | ||||||
![]() | VIRAL PROTEIN / SHP | ||||||
Function / homology | Virus Head Decoration Protein; Chain: A, / Head decoration protein D / Head decoration protein D superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / viral capsid, decoration / Beta Barrel / Mainly Beta / Head decoration protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chang, C. / Forrer, P. / Ott, D. / Wlodawer, A. / Plueckthun, A. | ||||||
![]() | ![]() Title: Kinetic Stability and Crystal Structure of the Viral Capsid Protein SHP. Authors: Forrer, P. / Chang, C. / Ott, D. / Wlodawer, A. / Plueckthun, 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 | ![]() | 78 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 459.7 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1td0C ![]() 1td4C ![]() 1c5eS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 11988.448 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Na Acetate, PEG-MME 2000, MgSO4, glycine, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→60 Å / Num. all: 12968 / Num. obs: 12946 / % possible obs: 99.8 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.37→2.45 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1287 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C5E Resolution: 2.37→44.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 320802.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.2606 Å2 / ksol: 0.326792 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.37→44.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.52 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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