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- PDB-5d2w: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 5 ... -

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Basic information

Entry
Database: PDB / ID: 5d2w
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 5 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: 1.66 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: evolutionary changes in Kemp Eliminase KE07 - Crystal 5 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 1.1Sep 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.126, 97.126, 155.513
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-499-

HOH

21A-588-

HOH

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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) / Plasmid: pET29b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#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.: 201 / 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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11% (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: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→42.06 Å / Num. obs: 51184 / % possible obs: 98.86 % / Redundancy: 18.6 % / Biso Wilson estimate: 20.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.89
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.51 / CC1/2: 0.637 / % possible all: 93.03

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Processing

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

2rkx


Resolution: 1.66→42.057 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2607 5.09 %
Rwork0.1839 --
obs0.1855 51179 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→42.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 12 201 2154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162034
X-RAY DIFFRACTIONf_angle_d1.5142749
X-RAY DIFFRACTIONf_dihedral_angle_d12.453756
X-RAY DIFFRACTIONf_chiral_restr0.082312
X-RAY DIFFRACTIONf_plane_restr0.007357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.69020.2951120.29152329X-RAY DIFFRACTION92
1.6902-1.72270.30011300.27742379X-RAY DIFFRACTION94
1.7227-1.75790.34521380.26472429X-RAY DIFFRACTION95
1.7579-1.79610.27381300.25762475X-RAY DIFFRACTION97
1.7961-1.83790.30411310.2472505X-RAY DIFFRACTION99
1.8379-1.88380.28211420.23942541X-RAY DIFFRACTION100
1.8838-1.93480.28311540.23572546X-RAY DIFFRACTION100
1.9348-1.99170.21061350.21232550X-RAY DIFFRACTION100
1.9917-2.0560.26391380.20772557X-RAY DIFFRACTION100
2.056-2.12950.23811270.20082585X-RAY DIFFRACTION100
2.1295-2.21470.22931270.19612564X-RAY DIFFRACTION100
2.2147-2.31550.24511520.18812568X-RAY DIFFRACTION100
2.3155-2.43760.19221360.18422573X-RAY DIFFRACTION100
2.4376-2.59030.21791320.18332591X-RAY DIFFRACTION100
2.5903-2.79020.22861480.1872585X-RAY DIFFRACTION100
2.7902-3.07090.19971580.182603X-RAY DIFFRACTION100
3.0709-3.51510.19281360.16682641X-RAY DIFFRACTION100
3.5151-4.42790.17571370.14452698X-RAY DIFFRACTION100
4.4279-42.07030.17411440.14922853X-RAY DIFFRACTION100

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