+Open data
-Basic information
Entry | Database: PDB / ID: 3hoj | |||||||||
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Title | Crystal Structure of a Novel Engineered Retroaldolase: RA-22 | |||||||||
Components | RETROALDOLASE-22 | |||||||||
Keywords | LYASE / TIM BARREL / RETROALDOLASE / ENGINEERED COMPUTATIONALLY DESIGNED | |||||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | |||||||||
Biological species | artificial gene (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | |||||||||
Authors | Stoddard, B.L. / Doyle, L.A. | |||||||||
Citation | Journal: Science / Year: 2008 Title: De Novo Computational Design of Retro-Aldol Enzymes Authors: Jiang, L. / Althoff, E.A. / Clemente, F.R. / Doyle, L. / Rothlisberger, D. / Zanghellini, A. / Gallaher, J.L. / Betker, J.L. / Tanaka, F. / Barbas, C.F. / Hilvert, D. / Houk, K.N. / Stoddard, B.L. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hoj.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hoj.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 3hoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3hoj ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3hoj | HTTPS FTP |
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-Related 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: 28456.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) Description: THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS. Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: indole-3-glycerol-phosphate synthase |
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#2: 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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 27% PEG4000 FOLLOWED BY FURTHER EQUILIBRATION AFTER INITIAL CRYSTALLIZATION OVER 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 30% ...Details: 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 27% PEG4000 FOLLOWED BY FURTHER EQUILIBRATION AFTER INITIAL CRYSTALLIZATION OVER 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2007 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36.02 Å / Num. obs: 13187 / % possible obs: 98.9 % / Redundancy: 3.48 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 10.4 / Scaling rejects: 348 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.8 / Num. measured all: 3735 / Num. unique all: 1282 / Χ2: 1.15 / % possible all: 97.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.01 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.753 / SU B: 7.971 / SU ML: 0.205 / SU R Cruickshank DPI: 0.369 / SU Rfree: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.268 / 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 max: 63.68 Å2 / Biso mean: 25.724 Å2 / Biso min: 11.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→36.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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