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Open data
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Basic information
Entry | Database: PDB / ID: 3sva | ||||||
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Title | Crystal structure of V57D mutant of human cystatin C | ||||||
![]() | Cystatin-C | ||||||
![]() | hydrolase inhibitor / 3D domain swapping / cysteine protease inhibitor | ||||||
Function / homology | ![]() negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization ...negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization / negative regulation of proteolysis / Post-translational protein phosphorylation / defense response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / tertiary granule lumen / amyloid-beta binding / protease binding / vesicle / ficolin-1-rich granule lumen / Amyloid fiber formation / endoplasmic reticulum lumen / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orlikowska, M. / Szymanska, A. / Borek, D. / Otwinowski, Z. / Skowron, P. / Jankowska, E. | ||||||
![]() | ![]() Title: Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein. Authors: Orlikowska, M. / Szymanska, A. / Borek, D. / Otwinowski, Z. / Skowron, P. / Jankowska, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.6 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 445.7 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s67C ![]() 1g96S 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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Components
#1: Protein | Mass: 13381.098 Da / Num. of mol.: 1 / Mutation: V57D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Imidazole pH 6.5, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 4864 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 437 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G96 Resolution: 3.02→37.46 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU B: 31.204 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.464 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.02→37.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.02→3.095 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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