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- PDB-6ct3: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 27... -

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Basic information

Entry
Database: PDB / ID: 6ct3
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 27 round 7-2
ComponentsKemp eliminase
KeywordsLYASE / Kemp Eliminase / Directed Evolution / KE07 / DE NOVO PROTEIN
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-2-oxidanyl-benzenecarbonitrile
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: Nat Commun / Year: 2018
Title: The evolution of multiple active site configurations in a designed enzyme.
Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / ...Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / Kamerlin, S.C.L. / Jackson, C.J.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kemp eliminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9658
Polymers29,2401
Non-polymers7257
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.348, 80.348, 106.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Kemp eliminase


Mass: 29240.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-6VP / 5-nitro-2-oxidanyl-benzenecarbonitrile / 2-hydroxy-5-nitrobenzonitrile


Mass: 164.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4N2O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.5 M (NH4)2SO4, 0.8 M Li2SO4, 0.1 M Na3citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→19.7 Å / Num. obs: 28119 / % possible obs: 99.9 % / Redundancy: 26.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rrim(I) all: 0.26 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 26 % / Rmerge(I) obs: 0.115 / Num. unique obs: 1830 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D38

3d38


Resolution: 1.9→19.7 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.07
RfactorNum. reflection% reflection
Rfree0.2292 1378 5 %
Rwork0.2033 --
obs0.2046 27560 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 46 94 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212089
X-RAY DIFFRACTIONf_angle_d1.9122819
X-RAY DIFFRACTIONf_dihedral_angle_d22.808774
X-RAY DIFFRACTIONf_chiral_restr0.129314
X-RAY DIFFRACTIONf_plane_restr0.012361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.43341110.42662140X-RAY DIFFRACTION82
1.9679-2.04660.30861370.28932610X-RAY DIFFRACTION100
2.0466-2.13970.34771430.27992600X-RAY DIFFRACTION100
2.1397-2.25230.31131300.24972639X-RAY DIFFRACTION100
2.2523-2.39320.25521490.22682623X-RAY DIFFRACTION100
2.3932-2.57760.24841370.21182650X-RAY DIFFRACTION100
2.5776-2.83630.25721390.21532660X-RAY DIFFRACTION100
2.8363-3.24520.23241530.19872673X-RAY DIFFRACTION100
3.2452-4.08260.20251430.18272711X-RAY DIFFRACTION100
4.0826-19.7390.16521360.16272876X-RAY DIFFRACTION100

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