+Open data
-Basic information
Entry | Database: PDB / ID: 1gik | |||||||||
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Title | POKEWEED ANTIVIRAL PROTEIN FROM SEEDS | |||||||||
Components | ANTIVIRAL PROTEIN S | |||||||||
Keywords | HYDROLASE / ALPHA+BETA | |||||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / defense response to virus / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Phytolacca americana (American pokeweed) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Zeng, Z.H. / He, X.L. / Li, H.M. / Hu, Z. / Wang, D.C. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2003 Title: Crystal structure of pokeweed antiviral protein with well-defined sugars from seeds at 1.8 angstrom resolution Authors: Zeng, Z.H. / He, X.L. / Li, H.M. / Hu, Z. / Wang, D.C. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1998 Title: CRYSTALLIZATION AND PERLIMINARY CRYSTALLOGRAPHIC ANALYSES OF POKEWEED ANTIVIRAL PROTEIN FROM SEEDS Authors: Li, H.M. / Zeng, Z.H. / Hu, Z. / Wang, D.C. #2: Journal: SCI.CHINA, SER.C: LIFE SCI. / Year: 1998 Title: CRYSTAL STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN FROM SEEDS OF PHYTOLACCA AMERICANA AT 0.25 NM Authors: Zeng, Z.H. / JIN, L. / LI, H.M. / HU, Z. / Wang, D.C. #3: Journal: Eur.J.Biochem. / Year: 1994 Title: X-ray Structure of a Pokeweed Antiviral Protein, Coded by a New Genomic Clone, at 0.23 nm resolution. A Model Structure Provides a Suitable Electrostatic Field for Substrate Binding Authors: Ago, H. / Kataoka, J. / Tsuge, H. / Habuka, N. / Inagaki, E. / Noma, M. / Miyano, M. #4: Journal: J.Mol.Biol. / Year: 1993 Title: The 2.5 A Structure of Pokeweed Antiviral Protein Authors: Monzingo, A.F. / Collins, E.J. / Erust, S.R. / Irvin, J.D. / Robertus, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gik.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gik.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gik_validation.pdf.gz | 391 KB | Display | wwPDB validaton report |
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Full document | 1gik_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 1gik_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1gik_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gik ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gik | HTTPS FTP |
-Related structure data
Related structure data | 1pafS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29234.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / References: UniProt: P23339, rRNA N-glycosylase | ||
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#2: Sugar | #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: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 305 K / Method: evaporation / pH: 5.5 Details: PEG6000 SODIUM PHOSPHATE, pH 5.5, EVAPORATION, temperature 305K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 306 K / Method: vapor diffusionDetails: Li, H.M., (1998) ACTA CRYSTALLOGR.,SECT.D, 54, 137. PH range low: 6 / PH range high: 5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 22, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 19809 / Num. obs: 19619 / % possible obs: 69.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2 % / % possible all: 52.5 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 23204 / % possible obs: 82 % / Num. measured all: 68617 |
Reflection shell | *PLUS Lowest resolution: 1.88 Å / % possible obs: 69.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 8.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PAF Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2754268.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 23204 / σ(F): 0 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.88 Å / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.288 |