+Open data
-Basic information
Entry | Database: PDB / ID: 6roa | ||||||
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Title | Crystal structure of V57G mutant of human cystatin C | ||||||
Components | Cystatin-C | ||||||
Keywords | HYDROLASE / hydrolase inhibitor / monomeric structure | ||||||
Function / homology | Function and homology information negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / peptidase inhibitor activity / negative regulation of peptidase 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 / peptidase inhibitor activity / negative regulation of peptidase 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: 2.65 Å | ||||||
Authors | Orlikowska, M. / Behrendt, I. / Borek, D. / Otwinowski, Z. / Skowron, P. / Szymanska, A. | ||||||
Citation | Journal: Febs J. / Year: 2020 Title: NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution. Authors: Maszota-Zieleniak, M. / Jurczak, P. / Orlikowska, M. / Zhukov, I. / Borek, D. / Otwinowski, Z. / Skowron, P. / Pietralik, Z. / Kozak, M. / Szymanska, A. / Rodziewicz-Motowidlo, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6roa.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6roa.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 6roa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6roa ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6roa | HTTPS FTP |
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-Related structure data
Related structure data | 6rpvC 3nx0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13323.062 Da / Num. of mol.: 2 / Mutation: V57G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: pHD313 / Production host: Escherichia coli (E. coli) / Variant (production host): C41(DE3) / 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: 3.04 Å3/Da / Density % sol: 59.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 9095 / % possible obs: 96.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 47.82 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 9095 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NX0 Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.908 / SU B: 25.648 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.528 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→50 Å
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Refine LS restraints |
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