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- PDB-2bhx: Radiation damage of the Schiff base in phosphoserine aminotransfe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bhx | ||||||
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Title | Radiation damage of the Schiff base in phosphoserine aminotransferase (structure A) | ||||||
![]() | PHOSPHOSERINE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / RADIATION DAMAGE | ||||||
Function / homology | ![]() phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dubnovitsky, A.P. / Ravelli, R.B.G. / Popov, A.N. / Papageorgiou, A.C. | ||||||
![]() | ![]() Title: Strain Relief at the Active Site of Phosphoserine Aminotransferase Induced by Radiation Damage. Authors: Dubnovitsky, A.P. / Ravelli, R.B.G. / Popov, A.N. / Papageorgiou, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.8 KB | Display | ![]() |
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PDB format | ![]() | 133.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.3 KB | Display | ![]() |
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Full document | ![]() | 486.5 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bi1C ![]() 2bi2C ![]() 2bi3C ![]() 2bi5C ![]() 2bi9C ![]() 2biaC ![]() 2bieC ![]() 2bigC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40243.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL-5'-PHOSPHATE LINKED TO 196 / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 620 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-1PE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THIS ENTRY CONTAINS ONE OF NINE STRUCTURES THAT ARE DESCRIBED IN THE ACCOMPANYING JOURNAL ARTICLE. ...THIS ENTRY CONTAINS ONE OF NINE STRUCTURES |
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Sequence details | THE N-TERMINAL METHIONINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | pH: 8.2 Details: 30% PEG 400, 200 MM MGCL2, 5% GLYCEROL, 100 MM TRIS PH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→15 Å / Num. obs: 92486 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.68→1.72 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.68→15 Å / Num. parameters: 25447 / Num. restraintsaints: 23515 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: RESIDUES A 215, A 216, A 218, AND B 218 WERE MODELLED AS ALANINES. RESIDUES B 214, B 215,B 216 WERE NOT MODELLED
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Refine analyze | Num. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6280 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→15 Å
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Refine LS restraints |
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