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- PDB-5d38: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 17... -

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Basic information

Entry
Database: PDB / ID: 5d38
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 17 round 7-2
ComponentsDe novo kemp eliminase KE07 round 7-2
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: 1.427 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 17 round 7-2
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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo kemp eliminase KE07 round 7-2
B: De novo kemp eliminase KE07 round 7-2


Theoretical massNumber of molelcules
Total (without water)58,4812
Polymers58,4812
Non-polymers00
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint1 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.996, 81.290, 168.667
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 7-2


Mass: 29240.377 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.: 742 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% (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 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.427→23.41 Å / Num. obs: 100612 / % possible obs: 99.76 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.22

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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: 1.427→23.406 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 5020 4.99 %
Rwork0.1938 --
obs0.1955 100608 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.427→23.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 0 742 4842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064238
X-RAY DIFFRACTIONf_angle_d1.0885726
X-RAY DIFFRACTIONf_dihedral_angle_d12.0431564
X-RAY DIFFRACTIONf_chiral_restr0.068647
X-RAY DIFFRACTIONf_plane_restr0.008744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4266-1.44280.23881480.20873042X-RAY DIFFRACTION96
1.4428-1.45980.2371560.21063115X-RAY DIFFRACTION100
1.4598-1.47760.2521460.2083191X-RAY DIFFRACTION100
1.4776-1.49630.23551560.20413184X-RAY DIFFRACTION100
1.4963-1.5160.20591660.1923121X-RAY DIFFRACTION100
1.516-1.53670.2271860.19943128X-RAY DIFFRACTION100
1.5367-1.55870.21631530.19933202X-RAY DIFFRACTION100
1.5587-1.58190.24581760.19423133X-RAY DIFFRACTION100
1.5819-1.60670.23411630.19223153X-RAY DIFFRACTION100
1.6067-1.6330.221710.19143169X-RAY DIFFRACTION100
1.633-1.66110.22381580.19753153X-RAY DIFFRACTION100
1.6611-1.69130.21791720.19543180X-RAY DIFFRACTION100
1.6913-1.72390.19591720.19593143X-RAY DIFFRACTION100
1.7239-1.7590.21911600.19963184X-RAY DIFFRACTION100
1.759-1.79730.24381500.20143162X-RAY DIFFRACTION100
1.7973-1.83910.23911870.20323189X-RAY DIFFRACTION100
1.8391-1.8850.22351570.2093168X-RAY DIFFRACTION100
1.885-1.9360.25851780.21583180X-RAY DIFFRACTION100
1.936-1.99290.24511700.21213162X-RAY DIFFRACTION100
1.9929-2.05720.25121450.21443238X-RAY DIFFRACTION100
2.0572-2.13070.24661700.1973162X-RAY DIFFRACTION100
2.1307-2.21590.2021710.20363181X-RAY DIFFRACTION100
2.2159-2.31670.24071700.20053221X-RAY DIFFRACTION100
2.3167-2.43870.24831650.20813225X-RAY DIFFRACTION100
2.4387-2.59130.2231830.20433186X-RAY DIFFRACTION100
2.5913-2.79110.22341790.19823228X-RAY DIFFRACTION100
2.7911-3.07150.25171690.23207X-RAY DIFFRACTION100
3.0715-3.51460.22961650.17953287X-RAY DIFFRACTION100
3.5146-4.42320.19771880.15943277X-RAY DIFFRACTION100
4.4232-23.40920.20331900.17813417X-RAY DIFFRACTION99

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