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- PDB-6c7v: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22... -

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Basic information

Entry
Database: PDB / ID: 6c7v
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 22 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
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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
DepositionJan 23, 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 1.2Oct 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

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Assembly

Deposited unit
A: Kemp eliminase KE07


Theoretical massNumber of molelcules
Total (without water)27,9431
Polymers27,9431
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.968, 97.968, 155.927
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: 27943.068 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 277 K / Method: slow cooling / Details: 25 mM HEPES pH 7.25, 100 mM 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: 1.64→19.72 Å / Num. obs: 54654 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0244 / Rrim(I) all: 0.03454 / Net I/σ(I): 10.11
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 2 % / Rmerge(I) obs: 1.093 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 5353 / CC1/2: 0.309 / Rrim(I) all: 1.546 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSVERSION Jun 1, 2017data reduction
Aimlessversion 0.5.32data scaling
MOLREPVers 11.5.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D30

5d30


Resolution: 1.64→19.72 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.79
RfactorNum. reflection% reflection
Rfree0.2954 2698 4.94 %
Rwork0.2679 --
obs0.2693 54646 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 211 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072031
X-RAY DIFFRACTIONf_angle_d0.9222744
X-RAY DIFFRACTIONf_dihedral_angle_d2.1041680
X-RAY DIFFRACTIONf_chiral_restr0.067312
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.66980.38591510.35922668X-RAY DIFFRACTION100
1.6698-1.70190.36911550.3412653X-RAY DIFFRACTION100
1.7019-1.73660.3451300.3222699X-RAY DIFFRACTION100
1.7366-1.77440.29711230.29912711X-RAY DIFFRACTION100
1.7744-1.81560.30871460.28052690X-RAY DIFFRACTION100
1.8156-1.8610.30241360.27522685X-RAY DIFFRACTION100
1.861-1.91130.32411270.27232704X-RAY DIFFRACTION100
1.9113-1.96750.31811410.28652701X-RAY DIFFRACTION100
1.9675-2.03090.3251470.28182698X-RAY DIFFRACTION100
2.0309-2.10340.36961260.31332712X-RAY DIFFRACTION100
2.1034-2.18750.34751480.3142700X-RAY DIFFRACTION100
2.1875-2.28690.351380.36212740X-RAY DIFFRACTION100
2.2869-2.40730.43461490.35832711X-RAY DIFFRACTION100
2.4073-2.55780.34591450.31082746X-RAY DIFFRACTION100
2.5578-2.75490.26731330.25092757X-RAY DIFFRACTION100
2.7549-3.03120.24181590.22622745X-RAY DIFFRACTION100
3.0312-3.46780.23241580.2132779X-RAY DIFFRACTION100
3.4678-4.36120.2981500.25062829X-RAY DIFFRACTION100
4.3612-19.72310.2771360.25973020X-RAY DIFFRACTION100

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