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- PDB-5d2t: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 3 ... -

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Basic information

Entry
Database: PDB / ID: 5d2t
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 3 Wild Type
ComponentsDe novo designed kemp eliminase KE07
KeywordsDE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-2-oxidanyl-benzenecarbonitrile
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 1 Wild Type
Authors: Hong, N.-S. / Jackson, C.J. / Carr, P.D.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value
Revision 1.3Dec 25, 2024Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3242
Polymers29,1591
Non-polymers1641
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.338, 96.338, 155.323
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 De novo designed kemp eliminase KE07


Mass: 29159.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-6VP / 5-nitro-2-oxidanyl-benzenecarbonitrile / 2-hydroxy-5-nitrobenzonitrile


Mass: 164.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% (W/V) PEG 3350, 0.1M BIS-TRIS PROPANE, PH 8.5, 0.2M NAF

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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 210r / Detector: CCD / Date: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.87→46.007 Å / Num. obs: 35874 / % possible obs: 99.92 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.2201 / Net I/σ(I): 15.22

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RKX

2rkx


Resolution: 1.87→46.007 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1793 5 %
Rwork0.1906 --
obs0.1926 35873 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→46.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 12 193 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072070
X-RAY DIFFRACTIONf_angle_d1.0042798
X-RAY DIFFRACTIONf_dihedral_angle_d12.486769
X-RAY DIFFRACTIONf_chiral_restr0.044314
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.92060.36891190.35792569X-RAY DIFFRACTION100
1.9206-1.97710.32361230.31562569X-RAY DIFFRACTION100
1.9771-2.04090.2851450.23842557X-RAY DIFFRACTION100
2.0409-2.11380.2951300.26412582X-RAY DIFFRACTION100
2.1138-2.19850.22471450.19522587X-RAY DIFFRACTION100
2.1985-2.29850.29091280.22812575X-RAY DIFFRACTION100
2.2985-2.41970.23441390.18982591X-RAY DIFFRACTION100
2.4197-2.57130.22791480.1842600X-RAY DIFFRACTION100
2.5713-2.76980.23411260.1862623X-RAY DIFFRACTION100
2.7698-3.04850.21281580.17822611X-RAY DIFFRACTION100
3.0485-3.48950.22181380.17522651X-RAY DIFFRACTION100
3.4895-4.39580.20641480.15162697X-RAY DIFFRACTION100
4.3958-46.02130.20521460.16712868X-RAY DIFFRACTION100

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