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- PDB-5d32: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 11... -

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Basic information

Entry
Database: PDB / ID: 5d32
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 11 round 6
ComponentsDe novo kemp eliminase KE07 round 6
KeywordsDE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07
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: 2.1 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 11 round 6
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 kemp eliminase KE07 round 6
B: De novo kemp eliminase KE07 round 6


Theoretical massNumber of molelcules
Total (without water)58,3952
Polymers58,3952
Non-polymers00
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.881, 82.281, 170.934
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 De novo kemp eliminase KE07 round 6


Mass: 29197.264 Da / Num. of mol.: 2
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) / References: Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15% (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 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→18.96 Å / Num. obs: 32914 / % possible obs: 99.79 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1694 / Net I/σ(I): 10.55

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIV

3iiv


Resolution: 2.1→18.962 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1673 5.08 %
Rwork0.2 --
obs0.2025 32910 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→18.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 414 4394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074070
X-RAY DIFFRACTIONf_angle_d1.0275493
X-RAY DIFFRACTIONf_dihedral_angle_d14.2861497
X-RAY DIFFRACTIONf_chiral_restr0.039625
X-RAY DIFFRACTIONf_plane_restr0.004710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0995-2.16120.36471540.30472573X-RAY DIFFRACTION99
2.1612-2.23090.31161070.32162533X-RAY DIFFRACTION100
2.2309-2.31050.4411420.3492546X-RAY DIFFRACTION99
2.3105-2.40280.31111300.26542578X-RAY DIFFRACTION100
2.4028-2.5120.28521470.23612542X-RAY DIFFRACTION100
2.512-2.64410.32591300.23452595X-RAY DIFFRACTION100
2.6441-2.80920.31111390.22362593X-RAY DIFFRACTION100
2.8092-3.02530.2531300.20922601X-RAY DIFFRACTION100
3.0253-3.32830.25281430.18822594X-RAY DIFFRACTION100
3.3283-3.80650.22351380.16822640X-RAY DIFFRACTION100
3.8065-4.78310.16881700.14312635X-RAY DIFFRACTION100
4.7831-18.96270.20741430.1592807X-RAY DIFFRACTION100

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