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- PDB-3czt: Crystal Structure of S100B in the Calcium and Zinc Loaded State a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3czt | ||||||
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Title | Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9 | ||||||
![]() | Protein S100-B | ||||||
![]() | METAL BINDING PROTEIN / S100 / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ostendorp, T. / Diez, J. / Heizmann, C.W. / Fritz, G. | ||||||
![]() | ![]() Title: The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping. Authors: Ostendorp, T. / Diez, J. / Heizmann, C.W. / Fritz, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.7 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d0yC ![]() 3d10C ![]() 1mhoS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10727.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.02 M TAPS, pH 9.0, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→17.8 Å / Num. obs: 18236 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.159 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.42 |
Reflection shell | Resolution: 1.4→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 14292 / Num. unique all: 4340 / Num. unique obs: 4340 / % possible all: 89.4 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.434 / Cor.coef. Fo:Fc: 0.408
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1MHO Resolution: 1.4→17.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.678 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.039 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→17.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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