+Open data
-Basic information
Entry | Database: PDB / ID: 4a29 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the engineered retro-aldolase RA95.0 | ||||||
Components | ENGINEERED RETRO-ALDOL ENZYME RA95.0 | ||||||
Keywords | DE NOVO PROTEIN / ENGINEERED ENZYME / RETRO-ALDOLASE / 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 | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Giger, L. / Caner, S. / Kast, P. / Baker, D. / Ban, N. / Hilvert, D. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: Evolution of a designed retro-aldolase leads to complete active site remodeling. Authors: Giger, L. / Caner, S. / Obexer, R. / Kast, P. / Baker, D. / Ban, N. / Hilvert, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4a29.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4a29.ent.gz | 159.8 KB | Display | PDB format |
PDBx/mmJSON format | 4a29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a29_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4a29_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 4a29_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4a29_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/4a29 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a29 | HTTPS FTP |
-Related structure data
Related structure data | 4a2rC 4a2sC 1lblS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29710.219 Da / Num. of mol.: 1 / Fragment: TIM-BARREL FOLD, RESIDUES 1-258 Source method: isolated from a genetically manipulated source Details: ARTIFICIAL GENE. THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS. Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: Q06121*PLUS, indole-3-glycerol-phosphate synthase |
---|---|
#2: Chemical | ChemComp-3NK / |
#3: Chemical | ChemComp-MLT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
---|---|
Crystal grow | Temperature: 301 K / Method: vapor diffusion Details: 0.2 M DL-MALIC ACID PH 7.0, 20% W/V PEG 3350, 28 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 101040 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 34.14 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.21 / % possible all: 57.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LBL Resolution: 1.1→7.98 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 11.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.57 Å2 / ksol: 0.6 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→7.98 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|