+Open data
-Basic information
Entry | Database: PDB / ID: 1bry | ||||||
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Title | BRYODIN TYPE I RIP | ||||||
Components | BRYODIN I | ||||||
Keywords | RIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / BRYODIN | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | Bryonia dioica (red bryony) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Klei, H.E. / Chang, C.Y. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Molecular, biological, and preliminary structural analysis of recombinant bryodin 1, a ribosome-inactivating protein from the plant Bryonia dioica. Authors: Gawlak, S.L. / Neubauer, M. / Klei, H.E. / Chang, C.Y. / Einspahr, H.M. / Siegall, C.B. #1: Journal: Bioconjug.Chem. / Year: 1994 Title: Characterization of Ribosome-Inactivating Proteins Isolated from Bryonia Dioica and Their Utility as Carcinoma-Reactive Immunoconjugates Authors: Siegall, C.B. / Gawlak, S.L. / Chace, D. / Wolff, E.A. / Mixan, B. / Marquardt, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bry.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bry.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bry_validation.pdf.gz | 369.6 KB | Display | wwPDB validaton report |
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Full document | 1bry_full_validation.pdf.gz | 369.6 KB | Display | |
Data in XML | 1bry_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1bry_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1bry ftp://data.pdbj.org/pub/pdb/validation_reports/br/1bry | HTTPS FTP |
-Related structure data
Related structure data | 1tcsS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.962022, -0.161317, -0.220205), Vector: |
-Components
#1: Protein | Mass: 27202.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 1 - 247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bryonia dioica (red bryony) Description: CDNA SEQUENCE ISOLATED FROM BRYONIA DIOICA LEAF MRNA Organ: LEAF / Plasmid: PSE 13.0 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): LAMBDA DE3 / References: UniProt: P33185, rRNA N-glycosylase |
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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: 2.7 Å3/Da / Density % sol: 53 % Description: TRICHOSANTHIN MODEL TRUNCATED WITH PROGRAM MUTATE (S.SHERIFF) TO SELECT COMMON ATOMS BASED ON SEQUENCE ALIGNMENT. |
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Crystal grow | pH: 6 Details: 0.1M MES (PH 6.0), 23% MEPEG5K, 0.2M AMMONIUM SULFATE, 0.1M LICL |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Common name: PEG5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 2, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34 Å / Num. obs: 31074 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 8.7 / % possible all: 68.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TCS Resolution: 2.1→8 Å / σ(F): 1 Details: NCS RESTRAINTS BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT WERE USED FOR THE FIRST TWO REFINEMENT CYCLES BUT WERE REMOVED FOR ALL SUBSEQUENT CYCLES WHEN RFREE WAS SHOWN TO DECREASE BY ...Details: NCS RESTRAINTS BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT WERE USED FOR THE FIRST TWO REFINEMENT CYCLES BUT WERE REMOVED FOR ALL SUBSEQUENT CYCLES WHEN RFREE WAS SHOWN TO DECREASE BY APPROXIMATELY THE SAME AMOUNT AS R WHEN THE RESTRAINTS WERE REMOVED.
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Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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