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- PDB-6srz: Kemp Eliminase HG3.17 mutant Q50H, E47N, N300D Complexed with Tra... -

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Basic information

Entry
Database: PDB / ID: 6srz
TitleKemp Eliminase HG3.17 mutant Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
ComponentsKemp Eliminase HG3.17 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
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: 1.4 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

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Assembly

Deposited unit
A: Kemp Eliminase HG3.17 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
B: Kemp Eliminase HG3.17 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4566
Polymers68,9442
Non-polymers5124
Water10,809600
1
A: Kemp Eliminase HG3.17 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7283
Polymers34,4721
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG3.17 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7283
Polymers34,4721
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.000, 78.020, 98.050
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 Q50H, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole


Mass: 34471.844 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
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: 1.4→41.51 Å / Num. obs: 115115 / % possible obs: 99.99 % / Redundancy: 13.4 % / CC1/2: 0.998 / Net I/σ(I): 10.59
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 11380 / CC1/2: 0.475

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BS0

4bs0


Resolution: 1.4→41.51 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1827 --
Rwork0.1573 --
obs-115112 99.99 %
Refinement stepCycle: LAST / Resolution: 1.4→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 36 600 5140

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