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Yorodumi- PDB-1tij: 3D Domain-swapped human cystatin C with amyloid-like intermolecul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tij | ||||||
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Title | 3D Domain-swapped human cystatin C with amyloid-like intermolecular beta-sheets | ||||||
Components | Cystatin C | ||||||
Keywords | HYDROLASE INHIBITOR / HUMAN CYSTATIN C DIMER / 3D DOMAIN SWAPPING / AMYLOID FORMATION / INHIBITOR OF C1 AND C13 CYSTEINE PROTEASES / AMYLOID ANGIOPATHY / CEREBRAL HEMORRHAGE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å | ||||||
Authors | Janowski, R. / Kozak, M. / Abrahamson, M. / Grubb, A. / Jaskolski, M. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: 3D domain-swapped human cystatin C with amyloidlike intermolecular beta-sheets. Authors: Janowski, R. / Kozak, M. / Abrahamson, M. / Grubb, A. / Jaskolski, M. #1: Journal: Nat.Struct.Biol. / Year: 2001 Title: Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping Authors: Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Grubb, A. / Abrahamson, M. / Jaskolski, M. #2: Journal: To be Published Title: 3D domain swapping in n-truncated human cystatin C Authors: Janowski, R. / Abrahamson, M. / Grubb, A. / Jaskolski, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Expression of selenomethionyl derivative and preliminary crystallographic studies of human cystatin C Authors: Kozak, M. / Jankowska, E. / Janowski, R. / Grzonka, Z. / Grubb, A. / Alvarez Fernandez, M. / Abrahamson, M. / Jaskolski, M. #4: Journal: J.Mol.Biol. / Year: 1997 Title: NMR structural studies of human cystatin C dimers and monomers Authors: Ekiel, I. / Abrahamson, M. / Fulton, D.B. / Lindahl, P. / Storer, A.C. / Levadoux, W. / Lafrance, M. / Labelle, S. / Pomerleau, Y. / Groleau, D. / Lesauter, L. / Gehring, K. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS INTERTWINED TO FORM A 3D DOMAIN SWAPPED DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tij.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tij.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tij_validation.pdf.gz | 435.7 KB | Display | wwPDB validaton report |
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Full document | 1tij_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1tij_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1tij_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/1tij ftp://data.pdbj.org/pub/pdb/validation_reports/ti/1tij | HTTPS FTP |
-Related structure data
Related structure data | 1g96S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THIS ENTRY CORRESPONDS TO THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS, A AND B, INTERTWINED INTO A 3D DOMAIN-SWAPPED DIMER |
-Components
#1: Protein | Mass: 13365.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: PHD 313 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P01034 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 77.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100mM sodium acetate, 20mM CaCl2, 40-45% MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8885 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1996 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8885 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→40 Å / Num. all: 12273 / Num. obs: 12273 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 14 |
Reflection shell | Resolution: 3.03→3.08 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.2 / Num. unique all: 599 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ONE HALF OF HUMAN CYSTATIN C CRYSTALLOGRAPHIC DIMER WITH SWAPPED DOMAINS (PDB ENTRY 1G96) Resolution: 3.03→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 77294.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.969 Å2 / ksol: 0.271825 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.03→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.03→3.22 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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