+Open data
-Basic information
Entry | Database: PDB / ID: 3e7r | ||||||
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Title | X-ray Crystal Structure of Racemic Plectasin | ||||||
Components | Plectasin | ||||||
Keywords | ANTIMICROBIAL PROTEIN / plectasin / racemic protein crystallography / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Defensin / Secreted | ||||||
Function / homology | Function and homology information potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å | ||||||
Authors | Mandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.H. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods Authors: Mandal, K. / Pentelute, B.L. / Tereshko, V. / Thammavongsa, V. / Schneewind, O. / Kossiakoff, A.A. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e7r.cif.gz | 23.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e7r.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e7r_validation.pdf.gz | 405 KB | Display | wwPDB validaton report |
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Full document | 3e7r_full_validation.pdf.gz | 405 KB | Display | |
Data in XML | 3e7r_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 3e7r_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/3e7r ftp://data.pdbj.org/pub/pdb/validation_reports/e7/3e7r | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4415.024 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide is naturally found in Pseudoplectania nigrella (Ebony cup). References: UniProt: Q53I06 |
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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: 1.41 Å3/Da / Density % sol: 14.53 % |
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Crystal grow | Temperature: 292 K / pH: 7 Details: 0.1 M HEPES, 22.5% (w/v) Jeffamine ED-2001, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 22253 / % possible obs: 83.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.8 / % possible all: 32 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→22.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.522 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1→22.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.03 Å / Total num. of bins used: 20
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