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Open data
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Basic information
Entry | Database: PDB / ID: 1bry | ||||||
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Title | BRYODIN TYPE I RIP | ||||||
![]() | BRYODIN I | ||||||
![]() | RIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / BRYODIN | ||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Klei, H.E. / Chang, C.Y. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.6 KB | Display | ![]() |
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Full document | ![]() | 369.6 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tcsS S: Starting model for refinement |
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Similar structure data |
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Links
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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: |
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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.) ![]() Description: CDNA SEQUENCE ISOLATED FROM BRYONIA DIOICA LEAF MRNA Organ: LEAF / Plasmid: PSE 13.0 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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