+Open data
-Basic information
Entry | Database: PDB / ID: 5aou | ||||||
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Title | Structure of the engineered retro-aldolase RA95.5-8F apo | ||||||
Components | INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / RETRO-ALDOLASE / PROTEIN ENGINEERING / ENZYME DESIGN / DIRECTED EVOLUTION | ||||||
Function / homology | Function and homology information indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Obexer, R. / Mittl, P. / Hilvert, D. | ||||||
Citation | Journal: Nat Chem / Year: 2017 Title: Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Authors: Obexer, R. / Godina, A. / Garrabou, X. / Mittl, P.R. / Baker, D. / Griffiths, A.D. / Hilvert, D. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aou.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aou.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 5aou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/5aou ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5aou | HTTPS FTP |
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-Related structure data
Related structure data | 5an7C 4a2rS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29936.434 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE SEQUENCE WAS DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS. Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: Q06121, indole-3-glycerol-phosphate synthase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.54 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 0.1M SODIUM ACETATE TRIHYDRATE, 2M AMMONIUM SULFATE, PH 4.6, 20DEGREE CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→56.2 Å / Num. obs: 167431 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.96 |
-Processing
Software | Name: SHELXL / Classification: refinement | |||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A2R Resolution: 1.1→56.2 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.1→56.2 Å
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Refine LS restraints |
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