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- PDB-6cai: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 24... -

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Basic information

Entry
Database: PDB / ID: 6cai
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 24 round 7
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: 1.82 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 30, 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
B: Kemp Eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4893
Polymers58,3672
Non-polymers1221
Water6,125340
1
A: Kemp Eliminase KE07


Theoretical massNumber of molelcules
Total (without water)29,1831
Polymers29,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kemp Eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3052
Polymers29,1831
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.941, 82.412, 176.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kemp Eliminase KE07


Mass: 29183.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.1M Bis-tris propane pH 7.5, 0.2M NaF

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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: 1.82→47.799 Å / Num. obs: 51926 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.021 / Rrim(I) all: 0.0307 / Net I/σ(I): 12.5
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 10194 / CC1/2: 0.487 / Rrim(I) all: 0.93 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessversion 0.5.32data scaling
MOLREPVers 11.5.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D33

5d33


Resolution: 1.82→47.799 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2558 4.93 %
Rwork0.1984 --
obs0.2002 51923 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→47.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 8 340 4324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094127
X-RAY DIFFRACTIONf_angle_d0.9545578
X-RAY DIFFRACTIONf_dihedral_angle_d19.141531
X-RAY DIFFRACTIONf_chiral_restr0.065639
X-RAY DIFFRACTIONf_plane_restr0.006718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8550.37921360.33552738X-RAY DIFFRACTION100
1.855-1.89290.40941340.31662641X-RAY DIFFRACTION100
1.8929-1.9340.34111480.29392714X-RAY DIFFRACTION100
1.934-1.9790.3321330.2762711X-RAY DIFFRACTION100
1.979-2.02850.30511330.2592714X-RAY DIFFRACTION100
2.0285-2.08340.31011330.25422679X-RAY DIFFRACTION100
2.0834-2.14470.30071420.24482720X-RAY DIFFRACTION100
2.1447-2.21390.28561550.2382689X-RAY DIFFRACTION100
2.2139-2.2930.27261660.22122735X-RAY DIFFRACTION100
2.293-2.38480.31271290.21142699X-RAY DIFFRACTION100
2.3848-2.49340.28391390.21492733X-RAY DIFFRACTION100
2.4934-2.62480.29561390.22322740X-RAY DIFFRACTION100
2.6248-2.78920.26431480.22062753X-RAY DIFFRACTION100
2.7892-3.00460.26751300.21412757X-RAY DIFFRACTION100
3.0046-3.30690.23851310.20312771X-RAY DIFFRACTION100
3.3069-3.78520.21771550.1892773X-RAY DIFFRACTION100
3.7852-4.76830.17911500.15452828X-RAY DIFFRACTION100
4.7683-47.81580.16181570.15912970X-RAY DIFFRACTION100

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