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- PDB-6dc1: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25... -

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Entry
Database: PDB / ID: 6dc1
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 25 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 / 5-nitro-2-oxidanyl-benzenecarbonitrile / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 3, 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 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 KE07
B: Kemp eliminase KE07
C: Kemp eliminase KE07
D: Kemp eliminase KE07
E: Kemp eliminase KE07
F: Kemp eliminase KE07
G: Kemp eliminase KE07
H: Kemp eliminase KE07
I: Kemp eliminase KE07
J: Kemp eliminase KE07
K: Kemp eliminase KE07
L: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,75521
Polymers350,19912
Non-polymers1,5569
Water12,719706
1
A: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6303
Polymers29,1831
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3472
Polymers29,1831
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5723
Polymers29,1831
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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
5
E: 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
6
F: 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
7
G: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2892
Polymers29,1831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3472
Polymers29,1831
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: 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
10
J: 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
11
K: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3472
Polymers29,1831
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: 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)111.033, 111.033, 257.739
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Kemp eliminase KE07


Mass: 29183.256 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 715 molecules

#2: Chemical
ChemComp-6VP / 5-nitro-2-oxidanyl-benzenecarbonitrile / 2-hydroxy-5-nitrobenzonitrile


Mass: 164.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H4N2O3
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 0.1M Bis-trispropane 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
RadiationMonochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.68→47.26 Å / Num. obs: 99503 / % possible obs: 99.7 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.189 / Net I/σ(I): 9
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 9.5 % / Rmerge(I) obs: 4.5 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4967 / CC1/2: 0.345 / Rrim(I) all: 4.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
Aimlessversion 0.5.32data scaling
MOLREPVers 11.5.05; 04.08.2017phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D33

5d33


Resolution: 2.68→47.263 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 4993 5.07 %
Rwork0.2193 --
obs0.2199 98413 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→47.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23446 0 108 707 24261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924014
X-RAY DIFFRACTIONf_angle_d1.12632409
X-RAY DIFFRACTIONf_dihedral_angle_d22.338874
X-RAY DIFFRACTIONf_chiral_restr0.063732
X-RAY DIFFRACTIONf_plane_restr0.0064148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6801-2.71060.35221580.34063203X-RAY DIFFRACTION99
2.7106-2.74240.36141260.32583151X-RAY DIFFRACTION99
2.7424-2.77590.31661520.31343203X-RAY DIFFRACTION100
2.7759-2.8110.33161480.31523113X-RAY DIFFRACTION100
2.811-2.8480.32241780.30043167X-RAY DIFFRACTION100
2.848-2.8870.32811560.29393108X-RAY DIFFRACTION99
2.887-2.92820.3131400.27323197X-RAY DIFFRACTION99
2.9282-2.97190.28851700.26773120X-RAY DIFFRACTION100
2.9719-3.01840.30451720.26773148X-RAY DIFFRACTION100
3.0184-3.06790.29381960.25863121X-RAY DIFFRACTION99
3.0679-3.12070.29732180.25443100X-RAY DIFFRACTION100
3.1207-3.17750.27751560.25663212X-RAY DIFFRACTION100
3.1775-3.23860.24561420.24253107X-RAY DIFFRACTION100
3.2386-3.30470.2361800.2373140X-RAY DIFFRACTION100
3.3047-3.37650.27121960.24483172X-RAY DIFFRACTION100
3.3765-3.4550.29991590.27153118X-RAY DIFFRACTION99
3.455-3.54140.27361520.26693119X-RAY DIFFRACTION99
3.5414-3.63710.29661980.27793056X-RAY DIFFRACTION98
3.6371-3.74410.34481190.33932639X-RAY DIFFRACTION83
3.7441-3.86490.2671460.25463148X-RAY DIFFRACTION98
3.8649-4.0030.25481320.27822872X-RAY DIFFRACTION90
4.003-4.16320.23581840.2163104X-RAY DIFFRACTION100
4.1632-4.35250.221640.18823174X-RAY DIFFRACTION100
4.3525-4.58180.19251820.17663150X-RAY DIFFRACTION100
4.5818-4.86860.1911520.16953143X-RAY DIFFRACTION100
4.8686-5.24410.16582080.1553137X-RAY DIFFRACTION100
5.2441-5.7710.17611680.17163155X-RAY DIFFRACTION100
5.771-6.60410.21651920.19133139X-RAY DIFFRACTION100
6.6041-8.31310.18991840.17943129X-RAY DIFFRACTION100
8.3131-47.27070.15531650.1563075X-RAY DIFFRACTION98

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