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Yorodumi- PDB-4jp7: High resolution structure of a papaya barwin-like protein (crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jp7 | |||||||||
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Title | High resolution structure of a papaya barwin-like protein (crystal form 2) | |||||||||
Components | papaya barwin-like protein | |||||||||
Keywords | UNKNOWN FUNCTION / pathogenesis-related protein of family 4 / barwin family / double-psi beta barrel | |||||||||
Function / homology | Function and homology information RNA nuclease activity / defense response to fungus / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Carica papaya (papaya) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å | |||||||||
Authors | Wohlkonig, A. / Wintjens, R. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: High-resolution structure of a papaya plant-defence barwin-like protein solved by in-house sulfur-SAD phasing. Authors: Huet, J. / Teinkela Mbosso, E.J. / Soror, S. / Meyer, F. / Looze, Y. / Wintjens, R. / Wohlkonig, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jp7.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jp7.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jp7 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jp7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13665.235 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: protein extracted from the latex of the plant Carica papaya Source: (natural) Carica papaya (papaya) / References: UniProt: U5HK42*PLUS #2: Chemical | ChemComp-GOL / | #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 | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 117408 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.98 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 1→1.11 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.94 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.05→39.53 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.977 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: 13.857 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→39.53 Å
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