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- PDB-4bs0: Crystal Structure of Kemp Eliminase HG3.17 E47N,N300D Complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bs0 | |||||||||
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Title | Crystal Structure of Kemp Eliminase HG3.17 E47N,N300D Complexed with Transition State Analog 6-Nitrobenzotriazole | |||||||||
![]() | KEMP ELIMINASE HG3.17 | |||||||||
![]() | LYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR COMPLEX / COMPUTATIONAL PROTEIN DESIGN / PROTON TRANSFER / KEMP ELIMINATION / DIRECTED EVOLUTION / TRANSITION STATE TUNING / BOTTOM-UP ENZYME CONSTRUCTION / ELEMENTARY CHEMICAL STEP CATALYSIS | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Blomberg, R. / Kries, H. / Pinkas, D.M. / Mittl, P.R.E. / Gruetter, M.G. / Privett, H.K. / Mayo, S. / Hilvert, D. | |||||||||
![]() | ![]() Title: Precision is Essential for Efficient Catalysis in an Evolved Kemp Eliminase Authors: Blomberg, R. / Kries, H. / Pinkas, D.M. / Mittl, P.R.E. / Gruetter, M.G. / Privett, H.K. / Mayo, S.L. / 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. THE SHEETS PRESENTED AS "BA" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 517.3 KB | Display | ![]() |
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PDB format | ![]() | 448.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 473.5 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nydS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34461.824 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: KEMP ELIMINASE HG-2 (PDB ID 3NYD) WITH MUTATION V6I, Q37K, K50Q, G82A, M84C, S89N, Q90F, T105I, A125T, T142N, T208M, S265T, F267M, W275A, R276F, T279S Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 1.1 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 5.9, SEEDING |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→28.3 Å / Num. obs: 225765 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 9.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.09→1.13 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / % possible all: 57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NYD Resolution: 1.09→28.339 Å / SU ML: 0.08 / σ(F): 1.92 / Phase error: 13.99 / Stereochemistry target values: LS_WUNIT_K1 Details: THE MAXIMUM-LIKELIHOOD TARGET FUNCTION WAS USED WITH OPTIMIZED STEREOCHEMICAL AND ATOMIC-DISPLACEMENT PARAMETER RESTRAINTS FOR THE MAJORITY OF THE REFINEMENT. IN THE FINAL STAGE, THE LIGAND ...Details: THE MAXIMUM-LIKELIHOOD TARGET FUNCTION WAS USED WITH OPTIMIZED STEREOCHEMICAL AND ATOMIC-DISPLACEMENT PARAMETER RESTRAINTS FOR THE MAJORITY OF THE REFINEMENT. IN THE FINAL STAGE, THE LIGAND AS WELL AS THE CATALYTIC RESIDUES ASP127 AND GLN50 FOR THE A-CHAIN WERE REFINED UNRESTRAINED, USING THE LEAST SQUARES TARGET FUNCTION.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: PHENIX V1.8.2-1309 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→28.339 Å
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Refine LS restraints |
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LS refinement shell |
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