[English] 日本語
Yorodumi- PDB-3ud6: Structural analyses of covalent enzyme-substrate analogue complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ud6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design | |||||||||
Components | RETRO-ALDOLASE | |||||||||
Keywords | LYASE/LYASE INHIBITOR / Computationally Designed / Retroaldolase / Tim Barrel / LYASE-LYASE INHIBITOR complex | |||||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE Function and homology information | |||||||||
Biological species | ARTIFICIAL GENE (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.091 Å | |||||||||
Authors | Baker, D. / Stoddard, B.L. / Althoff, E.A. / Wang, L. / Jiang, L. / Moody, J. / Bolduc, J. / Lassila, J. / Hilvert, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Authors: Wang, L. / Althoff, E.A. / Bolduc, J. / Jiang, L. / Moody, J. / Lassila, J.K. / Giger, L. / Hilvert, D. / Stoddard, B. / Baker, D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ud6.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ud6.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ud6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/3ud6 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/3ud6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3nxfC 3o6yC 1a53S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29736.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The Sequence Was Computationally Designed Based On Indole 3 Glycerol Phosphate Synthase Naturally Found in Sulfolobus Solfataricus. 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) | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-3NK / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 1-(6-METHOXY-2-NAPTHALENYL)-1,3-BUTANEDIONE (3NK) WAS REACTED WITH THE PROTEIN AND QUENCHED WITH ...1-(6-METHOXY-2-NAPTHALENY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: Protein at 5mg/ml in 100mm NaCl, 25mm TRIS pH7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mN Na acetate pH5.5, vapor diffusion, temperature 298k, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 18, 2009 / Details: VARIMAX HF |
Radiation | Monochromator: VARIMAX HR MIRRORS/OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.091→50 Å / Num. obs: 17137 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 29.82 Å2 / Rsym value: 0.037 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.091→2.16 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 6.86 / Rsym value: 0.153 / % possible all: 95.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A53, MODIFIED TO PREVENT MODEL BIAS Resolution: 2.091→19.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.894 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.268 Å / Luzzati d res low obs: 19.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.091→19.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.091→2.15 Å / Total num. of bins used: 20
|