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- PDB-6sry: Kemp Eliminase HG3.17 mutant Q50S, E47N, N300D Complexed with Tra... -

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Basic information

Entry
Database: PDB / ID: 6sry
TitleKemp Eliminase HG3.17 mutant Q50S, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
ComponentsKemp Eliminase HG3.17 Q50S, 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: 0.95 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 Q50S, E47N,N300D
B: Kemp Eliminase HG3.17 Q50S, E47N,N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2665
Polymers68,8422
Non-polymers4243
Water14,988832
1
A: Kemp Eliminase HG3.17 Q50S, E47N,N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6813
Polymers34,4211
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG3.17 Q50S, E47N,N300D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5852
Polymers34,4211
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.670, 77.590, 97.660
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 Q50S, E47N,N300D


Mass: 34420.773 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
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: X06SA / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.95→27.09 Å / Num. obs: 358809 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.993 / Net I/σ(I): 7.62
Reflection shellResolution: 0.95→0.984 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 35635 / CC1/2: 0.469

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Processing

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

4bs0


Resolution: 0.95→27.086 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1701 --
Rwork0.1509 --
obs-358691 99.88 %
Refinement stepCycle: LAST / Resolution: 0.95→27.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 29 832 5461

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