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- PDB-2big: 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: 2big | ||||||
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Title | Radiation damage of the Schiff base in phosphoserine aminotransferase (structure I) | ||||||
![]() | 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 | ![]() | 325 KB | Display | ![]() |
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PDB format | ![]() | 274.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bhxC ![]() 2bi1C ![]() 2bi2C ![]() 2bi3C ![]() 2bi5C ![]() 2bi9C ![]() 2biaC ![]() 2bieC 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: 40374.754 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, 890 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PGE / | #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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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % |
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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: MARRESEARCH / Detector: CCD / Date: Jul 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.921 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→12 Å / Num. obs: 187887 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 96 |
Reflection shell | Resolution: 1.3→1.33 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.6 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.3→12 Å / Num. parameters: 59718 / Num. restraintsaints: 72392 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOUTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.035. RESIDUES A 215, A 216, A 218, AND B 218 WERE MODELLED AS ALANINES. RESIDUES A 1, A 2, B 1, B 2, B 214, B215 AND B 216 WERE NOT MODELLED.
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Refine analyze | Num. disordered residues: 31 / Occupancy sum hydrogen: 4936 / Occupancy sum non hydrogen: 6524 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→12 Å
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Refine LS restraints |
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