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- PDB-6dkv: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 21... -

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Basic information

Entry
Database: PDB / ID: 6dkv
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 21 round 5
ComponentsKemp eliminase KE07
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 / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Feb 12, 2020Group: 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 1.3Oct 11, 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 KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7054
Polymers29,3291
Non-polymers3763
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.266, 96.266, 155.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Kemp eliminase KE07


Mass: 29328.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 25 mM HEPES pH 7.25, 0.1M NaCl

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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: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→45.97 Å / Num. obs: 34667 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 35.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.023 / Rrim(I) all: 0.033 / Net I/σ(I): 19.69
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 2 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3379 / CC1/2: 0.483 / % possible all: 99.94

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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: 5D30

5d30


Resolution: 1.89→45.968 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.1982 1733 5 %
Rwork0.1879 --
obs0.1884 34663 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→45.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 26 245 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142174
X-RAY DIFFRACTIONf_angle_d1.3252942
X-RAY DIFFRACTIONf_dihedral_angle_d20.134822
X-RAY DIFFRACTIONf_chiral_restr0.086328
X-RAY DIFFRACTIONf_plane_restr0.01386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8901-1.94570.34441370.32472684X-RAY DIFFRACTION100
1.9457-2.00850.29651280.29222713X-RAY DIFFRACTION100
2.0085-2.08030.27141320.25992672X-RAY DIFFRACTION100
2.0803-2.16360.22081550.2232693X-RAY DIFFRACTION100
2.1636-2.26210.21521450.21232685X-RAY DIFFRACTION100
2.2621-2.38130.23051530.20332708X-RAY DIFFRACTION100
2.3813-2.53050.231590.20362717X-RAY DIFFRACTION100
2.5305-2.72590.21851560.19862704X-RAY DIFFRACTION100
2.7259-3.00010.19311480.18872746X-RAY DIFFRACTION100
3.0001-3.43420.18631290.19312790X-RAY DIFFRACTION100
3.4342-4.32620.19711390.15752823X-RAY DIFFRACTION100
4.3262-45.98150.15371520.16462995X-RAY DIFFRACTION100

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