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Open data
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Basic information
Entry | Database: PDB / ID: 3b5l | ||||||
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Title | Crystal Structure of a Novel Engineered Retroaldolase: RA-61 | ||||||
![]() | Endoxylanase | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | artificial gene (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stoddard, B.L. / Doyle, L.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hojC ![]() 1m4wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21916.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) Description: Computationally designed based on the structure of thermophilic b-1,4-xylanase from Nonomuraea flexuosa Plasmid: pET29b / Production host: ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow![]() |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2007 / Details: Mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→46.73 Å / Num. all: 16489 / Num. obs: 16082 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.96 / Net I/σ(I): 12 / Scaling rejects: 424 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.45 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.1 / Num. measured all: 3300 / Num. unique all: 1347 / Χ2: 0.81 / % possible all: 83.3 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: TRUNCATED 1m4w Resolution: 1.8→33.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.799 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.154 / 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: 17.723 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -5.8322 Å / Origin y: -10.112 Å / Origin z: 13.7669 Å
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