+Open data
-Basic information
Entry | Database: PDB / ID: 1ivy | |||||||||
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Title | PHYSIOLOGICAL DIMER HPP PRECURSOR | |||||||||
Components | HUMAN PROTECTIVE PROTEIN | |||||||||
Keywords | CARBOXYPEPTIDASE / SERINE CARBOXYPEPTIDASE / PROTECTIVE PROTEIN / GLYCOPROTEIN / ZYMOGEN | |||||||||
Function / homology | Function and homology information carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / regulation of chaperone-mediated autophagy / Sialic acid metabolism / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation / lysosomal lumen / intracellular protein transport / regulation of protein stability / azurophil granule lumen / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular exosome / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, TWO-FOLD AVERAGING / Resolution: 2.2 Å | |||||||||
Authors | Rudenko, G. / Bonten, E. / D'Azzo, A. / Hol, W.G.J. | |||||||||
Citation | Journal: Structure / Year: 1995 Title: Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism. Authors: Rudenko, G. / Bonten, E. / d'Azzo, A. / Hol, W.G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure Determination of the Human Protective Protein: Twofold Averaging Reveals the Three-Dimensional Structure of a Domain which Was Entirely Absent in the Initial Model Authors: Rudenko, G. / Bonten, E. / D'Azzo, A. / Hol, W.G.J. #2: Journal: Cell(Cambridge,Mass.) / Year: 1988 Title: Expression of Cdna Encoding the Human 'Protective Protein' Associated with Lysosomal Beta-Galactosidase and Neuraminidase: Homology to Yeast Proteases Authors: Galjart, N.J. / Gillemans, N. / Harris, A. / Van Der Horst, G.T. / Verheijen, F.W. / Galjaard, H. / D'Azzo, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivy.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivy.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ivy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ivy_validation.pdf.gz | 545 KB | Display | wwPDB validaton report |
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Full document | 1ivy_full_validation.pdf.gz | 557.6 KB | Display | |
Data in XML | 1ivy_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1ivy_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivy ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51486.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: BACULOVIRUS MEDIATED OVER-EXPRESSION. SEE BONTEN ET AL. 1995, J.B.C. 270, P. 26441-26445 Cell line: SF21 / Gene: HUPP54 / Gene (production host): HUPP54 / Production host: SF21 INSECT CELLS / References: UniProt: P10619, carboxypeptidase C #2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: 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: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 285 K / pH: 8.3 Details: PEG 8000, PH 8.0 - 8.3 AT 4 - 12 DEGREES CELSIUS, temperature 285K |
Crystal grow | *PLUS Method: unknown / PH range low: 8.3 / PH range high: 8 |
Components of the solutions | *PLUS Common name: PEG8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.3 Å / Num. obs: 67740 / % possible obs: 95.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 6 % / Mean I/σ(I) obs: 5.7 / Rsym value: 0.13 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 436709 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, TWO-FOLD AVERAGING Starting model: SERINE CARBOXYPEPTIDASE FROM WHEAT Resolution: 2.2→8 Å Details: RESIDUES ASN B 216 AND LEU B 217 ARE IN AN AREA OF POOR ELECTRON DENSITY. THE EXACT GEOMETRY OF THESE RESIDUES IS NOT CLEAR FROM THE ELECTRON DENSITY MAP, BUT THEIR GENERAL POSITION IS. IN ...Details: RESIDUES ASN B 216 AND LEU B 217 ARE IN AN AREA OF POOR ELECTRON DENSITY. THE EXACT GEOMETRY OF THESE RESIDUES IS NOT CLEAR FROM THE ELECTRON DENSITY MAP, BUT THEIR GENERAL POSITION IS. IN ADDITION, THE RESTRAINING DISULFIDE CYS 213 - CYS 218 SUPPORTS THE DEPOSITORS' MODEL IN THIS AREA.
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Refine analyze | Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å /
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Total num. of bins used: 8 / Rfactor obs: 0.24 |