+Open data
-Basic information
Entry | Database: PDB / ID: 2p4e | ||||||
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Title | Crystal Structure of PCSK9 | ||||||
Components | Proprotein convertase subtilisin/kexin type 9 | ||||||
Keywords | HYDROLASE / protease / subtilisin / LDL receptor / LDL / endocytosis | ||||||
Function / homology | Function and homology information adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Cunningham, D. / Danley, D.E. / Geoghegan, F.K. / Griffor, M.C. / Hawkins, J.L. / Qiu, X. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia. Authors: Cunningham, D. / Danley, D.E. / Geoghegan, K.F. / Griffor, M.C. / Hawkins, J.L. / Subashi, T.A. / Varghese, A.H. / Ammirati, M.J. / Culp, J.S. / Hoth, L.R. / Mansour, M.N. / McGrath, K.M. / ...Authors: Cunningham, D. / Danley, D.E. / Geoghegan, K.F. / Griffor, M.C. / Hawkins, J.L. / Subashi, T.A. / Varghese, A.H. / Ammirati, M.J. / Culp, J.S. / Hoth, L.R. / Mansour, M.N. / McGrath, K.M. / Seddon, A.P. / Shenolikar, S. / Stutzman-Engwall, K.J. / Warren, L.C. / Xia, D. / Qiu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4e.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4e.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 2p4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p4e_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 2p4e_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 2p4e_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 2p4e_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4e ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4e | HTTPS FTP |
-Related structure data
Related structure data | 1ic6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 74461.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Plasmid: PCSK9 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #3: 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 grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 1500, 50 mM Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2006 / Details: mirros |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→75 Å / Num. all: 48000 / Num. obs: 46285 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IC6 Resolution: 1.98→75 Å / Isotropic thermal model: individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→75 Å
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Refine LS restraints |
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