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- PDB-6ss3: Kemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Tra... -

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Basic information

Entry
Database: PDB / ID: 6ss3
TitleKemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
ComponentsKemp Eliminase HG3.17 Q50K, E47N, N300D
KeywordsDE NOVO PROTEIN / Kemp Eliminase / Enzyme / Protein Design
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBloch, J.S. / Pinkas, D.M. / Hilvert, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Catalysis / Year: 2020
Title: Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency
Authors: Kries, H. / Bloch, J.S. / Bunzel, H.A. / Pinkas, D.M. / Hilvert, D.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kemp Eliminase HG3.17 Q50K, E47N, N300D
B: Kemp Eliminase HG3.17 Q50K, E47N, N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5347
Polymers68,9262
Non-polymers6085
Water10,719595
1
A: Kemp Eliminase HG3.17 Q50K, E47N, N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8154
Polymers34,4631
Non-polymers3523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG3.17 Q50K, E47N, N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7193
Polymers34,4631
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.080, 78.280, 98.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Kemp Eliminase HG3.17 Q50K, E47N, N300D


Mass: 34462.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.1 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 5.9, SEEDING

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.15→47.68 Å / Num. obs: 207219 / % possible obs: 99.98 % / Redundancy: 13.2 % / Biso Wilson estimate: 11.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.71
Reflection shellResolution: 1.15→1.191 Å / Num. unique obs: 20488 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BS0

4bs0


Resolution: 1.15→47.68 Å / SU ML: 0.1126 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1581 10465 5.05 %
Rwork0.1381 196735 -
obs0.1391 207200 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.39 Å2
Refinement stepCycle: LAST / Resolution: 1.15→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 41 595 5230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01255585
X-RAY DIFFRACTIONf_angle_d1.25547721
X-RAY DIFFRACTIONf_chiral_restr0.0925828
X-RAY DIFFRACTIONf_plane_restr0.00871052
X-RAY DIFFRACTIONf_dihedral_angle_d14.86112092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.2943730.26186427X-RAY DIFFRACTION99.88
1.16-1.180.28583160.25496494X-RAY DIFFRACTION99.97
1.18-1.190.27783790.256500X-RAY DIFFRACTION99.99
1.19-1.210.27913320.23526520X-RAY DIFFRACTION100
1.21-1.220.23633100.22416522X-RAY DIFFRACTION99.99
1.22-1.240.22333140.21866538X-RAY DIFFRACTION99.99
1.24-1.260.24423670.21516508X-RAY DIFFRACTION99.99
1.26-1.280.2373280.21696500X-RAY DIFFRACTION99.99
1.28-1.30.24193250.19996529X-RAY DIFFRACTION99.97
1.3-1.320.23063550.19486501X-RAY DIFFRACTION99.99
1.32-1.340.2043650.17466486X-RAY DIFFRACTION99.99
1.34-1.360.19363650.16136531X-RAY DIFFRACTION100
1.36-1.390.20853480.15036473X-RAY DIFFRACTION100
1.39-1.420.18433240.14216585X-RAY DIFFRACTION100
1.42-1.450.15713430.13086530X-RAY DIFFRACTION100
1.45-1.480.15843620.12526500X-RAY DIFFRACTION99.97
1.48-1.520.14663180.12496560X-RAY DIFFRACTION100
1.52-1.560.16173830.12176539X-RAY DIFFRACTION100
1.56-1.610.14263590.10826513X-RAY DIFFRACTION100
1.61-1.660.14253540.10256556X-RAY DIFFRACTION100
1.66-1.720.15253380.10226544X-RAY DIFFRACTION100
1.72-1.790.12753440.0966582X-RAY DIFFRACTION100
1.79-1.870.12543700.09656544X-RAY DIFFRACTION100
1.87-1.970.12953470.09986585X-RAY DIFFRACTION100
1.97-2.090.12913640.1036575X-RAY DIFFRACTION100
2.09-2.250.12083390.10236620X-RAY DIFFRACTION99.99
2.25-2.480.13073530.11156651X-RAY DIFFRACTION100
2.48-2.840.12763660.1216633X-RAY DIFFRACTION100
2.84-3.570.14113660.13866728X-RAY DIFFRACTION99.99

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