+Open data
-Basic information
Entry | Database: PDB / ID: 1cf5 | |||||||||
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Title | BETA-MOMORCHARIN STRUCTURE AT 2.55 A | |||||||||
Components | PROTEIN (BETA-MOMORCHARIN) | |||||||||
Keywords | RIBOSOME-INACTIVATING PROTEIN / RNA N-GLYCOSIDASE ACTIVITY / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Momordica charantia (bitter melon) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Yuan, Y.-R. / He, Y.-N. / Xiong, J.-P. / Xia, Z.-X. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Three-dimensional structure of beta-momorcharin at 2.55 A resolution. Authors: Yuan, Y.R. / He, Y.N. / Xiong, J.P. / Xia, Z.X. #1: Journal: Chin.Chem.Lett. / Year: 1995 Title: The Determination and Refinement of Three-Dimensional Structure of Beta- Momorcharin at 2.4 A Resolution Authors: Yuan, Y.-R. / Xiong, J.-P. / Xia, Z.-X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cf5.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cf5.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cf5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1cf5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1cf5_validation.xml.gz | 24 KB | Display | |
Data in CIF | 1cf5_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/1cf5 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/1cf5 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28122.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P29339, UniProt: P24817*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.49 Å3/Da / Density % sol: 50.52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 / Details: pH 6.10 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→40 Å / Num. obs: 17215 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.41→2.56 Å / % possible all: 30 |
Reflection shell | *PLUS % possible obs: 30 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→10 Å / Rfactor Rfree error: 0.011 / Cross valid method: IN THE LATE STAGE / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.55→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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