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- PDB-6dnj: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28... -

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Basic information

Entry
Database: PDB / ID: 6dnj
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5
ComponentsKemp eliminase KE07
KeywordsLYASE / Directed Evolution / DE NOVO PROTEIN
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-1,2-benzoxazole
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionJun 6, 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 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

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Assembly

Deposited unit
A: Kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6113
Polymers29,3291
Non-polymers2822
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.350, 97.350, 156.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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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.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-H5J / 5-nitro-1,2-benzoxazole


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.: 274 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 25 mM HEPES, pH 7.25, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→42 Å / Num. obs: 52414 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.13 / Net I/σ(I): 15.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 8.7 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2555 / CC1/2: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimless1.11.4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C7M

5c7m


Resolution: 1.65→43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.766 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18152 2666 5 %RANDOM
Rwork0.1716 ---
obs0.17212 50485 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.65→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 20 274 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192061
X-RAY DIFFRACTIONr_bond_other_d0.0010.022023
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9722787
X-RAY DIFFRACTIONr_angle_other_deg1.0223.0014650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78323.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02463
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9312.3591029
X-RAY DIFFRACTIONr_mcbond_other1.832.3521028
X-RAY DIFFRACTIONr_mcangle_it2.8173.5251295
X-RAY DIFFRACTIONr_mcangle_other2.983.5331296
X-RAY DIFFRACTIONr_scbond_it2.8672.8911032
X-RAY DIFFRACTIONr_scbond_other2.8662.891033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7534.1261493
X-RAY DIFFRACTIONr_long_range_B_refined4.16430.1492404
X-RAY DIFFRACTIONr_long_range_B_other4.16330.1422405
X-RAY DIFFRACTIONr_rigid_bond_restr2.66334084
X-RAY DIFFRACTIONr_sphericity_free11.0395114
X-RAY DIFFRACTIONr_sphericity_bonded12.70854207
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 193 -
Rwork0.328 3640 -
obs--99.9 %

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