+Open data
-Basic information
Entry | Database: PDB / ID: 3ndf | ||||||
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Title | Cleaved antitrypsin with P8-P6 Asp | ||||||
Components | (Alpha-1-antitrypsin) x 2 | ||||||
Keywords | HYDROLASE INHIBITOR / serpin | ||||||
Function / homology | Function and homology information Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Huntington, J.A. / Sendall, T.J. / Yamasaki, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2010 Title: Loop-sheet mechanism of serpin polymerization tested by reactive center loop mutations Authors: Yamasaki, M. / Sendall, T.J. / Harris, L.E. / Lewis, G.M.W. / Huntington, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ndf.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndf.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ndf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ndf_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 3ndf_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 3ndf_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3ndf_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndf ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndf | HTTPS FTP |
-Related structure data
Related structure data | 3nddC 1ezxS 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: 38544.605 Da / Num. of mol.: 1 Fragment: P1 cleaved antitrypsin, nterm, UNP residues 46-382 Mutation: C232A, M351D, F352D, L353D, M358R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pCEP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01009 |
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#2: Protein/peptide | Mass: 4139.938 Da / Num. of mol.: 1 Fragment: P1 cleaved antitrypsin, cterm, UNP residues 383-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pCEP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01009 |
#3: 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: 2.2 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 0.12M Alcohols (Morpheus), 0.1M Buffer 1, 13.3% PEG 550MME, 6.6% PEG 20000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 12, 2009 |
Radiation | Monochromator: Xenocs FOX2D Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.8 Å / Num. all: 9871 / Num. obs: 9871 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 6.1 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZX Resolution: 2.7→48.8 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.849 / SU B: 14.082 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / 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: 20.298 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→48.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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