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- PDB-6c7m: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 19... -

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Basic information

Entry
Database: PDB / ID: 6c7m
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 19 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: 1.45 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 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 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6834
Polymers29,3291
Non-polymers3553
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.664, 96.664, 156.182
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.25 / 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 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.45→19.69 Å / Num. obs: 76007 / % possible obs: 99.09 % / Redundancy: 2 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01004 / Rrim(I) all: 0.0142 / Net I/σ(I): 30.07
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7378 / Mean I/σ(I) obs: 1 / Num. unique obs: 7064 / CC1/2: 0.488 / Rrim(I) all: 1.043 / % possible all: 93.84

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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: 1.45→19.69 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.1985 3792 4.99 %
Rwork0.1834 --
obs0.1841 76001 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 24 298 2274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072140
X-RAY DIFFRACTIONf_angle_d0.892902
X-RAY DIFFRACTIONf_dihedral_angle_d20.633811
X-RAY DIFFRACTIONf_chiral_restr0.088323
X-RAY DIFFRACTIONf_plane_restr0.005379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46840.29631400.322459X-RAY DIFFRACTION92
1.4684-1.48770.33111010.31532515X-RAY DIFFRACTION94
1.4877-1.50810.291300.29472547X-RAY DIFFRACTION96
1.5081-1.52960.3111390.27242583X-RAY DIFFRACTION97
1.5296-1.55240.26951480.25532576X-RAY DIFFRACTION98
1.5524-1.57670.271300.24242644X-RAY DIFFRACTION99
1.5767-1.60250.25281350.23462649X-RAY DIFFRACTION100
1.6025-1.63010.23951330.22232665X-RAY DIFFRACTION100
1.6301-1.65970.24081310.222686X-RAY DIFFRACTION100
1.6597-1.69170.20811680.21182629X-RAY DIFFRACTION100
1.6917-1.72620.24881360.20922679X-RAY DIFFRACTION100
1.7262-1.76370.19351440.20242650X-RAY DIFFRACTION100
1.7637-1.80470.24621070.20122693X-RAY DIFFRACTION100
1.8047-1.84980.19841340.19492691X-RAY DIFFRACTION100
1.8498-1.89980.22951650.19492643X-RAY DIFFRACTION100
1.8998-1.95560.21411420.19932684X-RAY DIFFRACTION100
1.9556-2.01870.19261390.19062702X-RAY DIFFRACTION100
2.0187-2.09070.20591440.19132676X-RAY DIFFRACTION100
2.0907-2.17440.18971180.18392710X-RAY DIFFRACTION100
2.1744-2.27320.1781590.17862682X-RAY DIFFRACTION100
2.2732-2.39290.20821370.18372731X-RAY DIFFRACTION100
2.3929-2.54250.1991490.1862711X-RAY DIFFRACTION100
2.5425-2.73830.18411490.19062715X-RAY DIFFRACTION100
2.7383-3.01310.17041480.17832756X-RAY DIFFRACTION100
3.0131-3.44710.18851520.16932753X-RAY DIFFRACTION100
3.4471-4.33570.18841600.14982799X-RAY DIFFRACTION100
4.3357-19.95820.18691540.16932981X-RAY DIFFRACTION100

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