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Yorodumi- PDB-1p9g: Crystal structure of a novel antifungal protein distinct with fiv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p9g | |||||||||
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Title | Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Ecommia ulmoides Oliver at atomic resolution | |||||||||
Components | EAFP 2 | |||||||||
Keywords | ANTIFUNGAL PROTEIN / ANTIFUNGAL PEPTIDE / ATOMIC RESOLUTION | |||||||||
Function / homology | Function and homology information chitin binding / defense response to fungus / killing of cells of another organism Similarity search - Function | |||||||||
Biological species | Eucommia ulmoides (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.84 Å | |||||||||
Authors | Xiang, Y. / Huang, R.H. / Liu, X.Z. / Wang, D.C. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2004 Title: Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution. Authors: Xiang, Y. / Huang, R.H. / Liu, X.Z. / Zhang, Y. / Wang, D.C. | |||||||||
History |
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Remark 999 | It appears that this protein sequence has not been deposited in the sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9g.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9g.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p9g_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 1p9g_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 1p9g_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1p9g_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9g ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9g | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4172.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eucommia ulmoides (plant) / Tissue: tree bark / References: UniProt: P83597 | ||
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#2: Chemical | #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: 1.39 Å3/Da / Density % sol: 23.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: SODIUM ACETATE, ISO-PROPANOL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2002 |
Radiation | Monochromator: Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.84→100 Å / Num. all: 22113 / Num. obs: 22113 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 0.84→0.87 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8.5 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.84→100 Å / Num. parameters: 3401 / Num. restraintsaints: 3876 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 StereochEM target val spec case: CSD L-PYROGLUTAMIC ACID DATA FOR PCA Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 249 / Occupancy sum non hydrogen: 345.5 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.84→100 Å
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Refine LS restraints |
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LS refinement shell |
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