+Open data
-Basic information
Entry | Database: PDB / ID: 1rn7 | ||||||
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Title | Structure of human cystatin D | ||||||
Components | Cystatin D | ||||||
Keywords | PROTEIN BINDING / inhibitor of cysteine peptidases / cystatin D | ||||||
Function / homology | Function and homology information cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Alvarez-Fernandez, M. / Liang, Y.H. / Abrahamson, M. / Su, X.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of human cystatin D, a cysteine peptidase inhibitor with restricted inhibition profile. Authors: Alvarez-Fernandez, M. / Liang, Y.H. / Abrahamson, M. / Su, X.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rn7.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rn7.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rn7 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rn7 | HTTPS FTP |
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-Related structure data
Related structure data | 1roaC 1cewS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 13927.619 Da / Num. of mol.: 1 / Mutation: C26R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: parotid gland / Plasmid: pHD389 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P28325 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris-HCl, PEG400, (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 5243 / Num. obs: 4955 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.252 / Num. unique all: 467 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CEW Resolution: 2.5→28.16 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 560375.71 / 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: 62.6499 Å2 / ksol: 0.344637 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→28.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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