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Yorodumi- PDB-3zrp: Crystal structure and substrate specificity of a thermophilic arc... -
+Open data
-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 | ||||||
Components | SERINE-PYRUVATE AMINOTRANSFERASE (AGXT) | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sayer, C. / Bommer, M. / Isupov, M.N. / Ward, J. / Littlechild, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zrp.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zrp.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zrp ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zrp | HTTPS FTP |
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-Related structure data
Related structure data | 3zrqC 3zrrC 2bkwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q97VM5, serine-pyruvate transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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