+Open data
-Basic information
Entry | Database: PDB / ID: 1kn3 | ||||||
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Title | Murine PEBP-2 (phosphatidylethanolamine-binding protein-2) | ||||||
Components | Phosphatidylethanolamine Binding Protein-2 | ||||||
Keywords | PROTEIN BINDING / Phosphatidylethanolamine binding / Raf-1 kinase inhibitor / Cis-peptide | ||||||
Function / homology | Function and homology information negative regulation of MAPK cascade / serine-type endopeptidase inhibitor activity / lipid binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Simister, P.C. / Banfield, M.J. / Brady, R.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family. Authors: Simister, P.C. / Banfield, M.J. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kn3.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kn3.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kn3_validation.pdf.gz | 426.6 KB | Display | wwPDB validaton report |
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Full document | 1kn3_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 1kn3_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1kn3_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1kn3 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1kn3 | HTTPS FTP |
-Related structure data
Related structure data | 1bd9S 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: 20777.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: pebp-2 / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VIN1 |
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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: 2.01 Å3/Da / Density % sol: 38.87 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 200mM sodium acetate trihydrate, 100mM Tris.HCl, pH 8.5, VAPOUR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2001 / Details: Mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 16223 / Num. obs: 15638 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.26 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 8.5 / % possible all: 92.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 92.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BD9 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.926 / SU B: 3.94 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 13.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.923 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 10.3695 Å / Origin y: 22.7567 Å / Origin z: 11.8122 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor all: 0.21315 / Rfactor obs: 0.21 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 |