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- PDB-3zrp: Crystal structure and substrate specificity of a thermophilic arc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zrp | ||||||
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Title | Crystal structure and substrate specificity of a thermophilic archaeal serine : pyruvate aminotransferase from Sulfolobus solfataricus | ||||||
![]() | SERINE-PYRUVATE AMINOTRANSFERASE (AGXT) | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() serine-pyruvate transaminase / glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / peroxisome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sayer, C. / Bommer, M. / Isupov, M.N. / Ward, J. / Littlechild, J. | ||||||
![]() | ![]() Title: Crystal Structure and Substrate Specificity of the Thermophilic Serine:Pyruvate Aminotransferase from Sulfolobus Solfataricus Authors: Sayer, C. / Bommer, M. / Isupov, M.N. / Ward, J. / Littlechild, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.2 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 473 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zrqC ![]() 3zrrC ![]() 2bkwS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 42028.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % / Description: NONE |
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Crystal grow | pH: 7 Details: 5 MG/ML PROTEIN, 50 MM TRIS HCL PH 8.5 AND 15% POLYETHYLENE GLYCOL (PEG) 400. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→24 Å / Num. obs: 76065 / % possible obs: 95 % / Observed criterion σ(I): 1.6 / Redundancy: 2.7 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 76.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BKW Resolution: 1.75→94.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.221 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.366 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→94.87 Å
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Refine LS restraints |
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