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- PDB-1dwf: Study on radiation damage on a cryocooled crystal. Part 2: Struct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dwf | |||||||||
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Title | Study on radiation damage on a cryocooled crystal. Part 2: Structure after irradiation with 9.1*10e15 photons/mm2 | |||||||||
![]() | MYROSINASE MA1 | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / RADIATION DAMAGE / RADIOLYSIS / CRYO-COOLED | |||||||||
Function / homology | ![]() thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Burmeister, W.P. | |||||||||
![]() | ![]() Title: Structural Changes in a Cryo-Cooled Protein Crystal due to Radiation Damage Authors: Burmeister, W.P. #1: ![]() Title: The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Side Machinery of an S-Glycosidase Authors: Burmeister, W.P. / Cottaz, S. / Driguez, H. / Iori, R. / Palmieri, S. / Henrissat, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.8 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1dwaC ![]() 1dwgC ![]() 1dwhC ![]() 1dwiC ![]() 1dwjC ![]() 1myrS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 1 types, 1 molecules M
#1: Protein | Mass: 56848.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-501 / Source method: isolated from a natural source Details: AFTER IRRADIATION WITH 9.1*10E15 PHOTONS/MM2 OF PHOTONS Source: (natural) ![]() |
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-Sugars , 4 types, 10 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 802 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-ZN / | ||||
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#7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
-Details
Compound details | THIS ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES IN A STUDY ON RADIATION DAMAGE IN CRYO- ...THIS ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES | ||
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Nonpolymer details | GLYCOSYLATSequence details | THERE ARE SOME DISCREPANCIES IN THE SEQUENCE COMPARED TO ENTRY 1MYR AS THE X-RAY SEQUENCE HAS BEEN ...THERE ARE SOME DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 50 % Description: DOSE 0.1*10E15 PHOTONS/MM2 USED FOR DATA COLLECTION, I/SIGMA VALUES ARE STRONGLY AFFECTED BY A FEW ZINGERS ON THE DETECTOR | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66% SATURATED AMMONIUM SULFATE, 100MM TRIS-HCL | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 1998 / Details: BENT MULTILAYER MIRROR, SAGITALLY FOCUSING CRYSTAL |
Radiation | Monochromator: C(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9475 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.9 Å / Num. obs: 51406 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % possible all: 99.8 |
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MYR Resolution: 2→17.4 Å / Rfactor Rfree error: 0.0034 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. ...Details: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. THE MODEL IS NOT SUPPOSED TO BE USED AS A MODEL OF MYROSINASE. A MODEL REPLACING ENTRY 1MYR WILL BE DEPOSITED LATER. NO COORDINATES ARE GIVEN FOR RESIDUES 1 - 2. PRO 501 IS THE LAST RESIDUE SEEN IN ELECTRON DENSITY. THE PROTEIN COULD EXTEND BEYOND PRO 501. THE OCCUPANCY OF CERTAIN GROUPS WHICH ARE SENSITIVE TO RADIATION DAMAGE HAS BEEN REFINED. DUE TO THIS REFINEMENT OCCUPANCIES DIFFERENT OR EVEN BIGGER THAT 1.0 ARE PRESENT IN THE STRUCTURE.
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→17.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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