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- PDB-5d2v: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 4 ... -

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Basic information

Entry
Database: PDB / ID: 5d2v
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 4 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
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 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 1.1Sep 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 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)29,1591
Polymers29,1591
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.437, 96.437, 155.148
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
Details: C-terminal-His6-tag is attached for purification / 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.: 181 / 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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES, pH 7.25, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→46.05 Å / Num. obs: 28621 / % possible obs: 99.84 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.1125 / Net I/σ(I): 13.31
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.57 / % possible all: 100

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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: 2.02→46.046 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1446 5.05 %
Rwork0.1902 --
obs0.1925 28615 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→46.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 0 181 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082030
X-RAY DIFFRACTIONf_angle_d1.0312743
X-RAY DIFFRACTIONf_dihedral_angle_d12.712755
X-RAY DIFFRACTIONf_chiral_restr0.039313
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0201-2.09230.3911450.31542671X-RAY DIFFRACTION100
2.0923-2.17610.29271430.27492643X-RAY DIFFRACTION100
2.1761-2.27510.28761320.21652667X-RAY DIFFRACTION100
2.2751-2.3950.25141320.19282688X-RAY DIFFRACTION100
2.395-2.54510.25631520.19932673X-RAY DIFFRACTION100
2.5451-2.74160.24721530.20262681X-RAY DIFFRACTION100
2.7416-3.01740.25761460.19872707X-RAY DIFFRACTION100
3.0174-3.45390.21771500.20122723X-RAY DIFFRACTION100
3.4539-4.35110.22921430.15982758X-RAY DIFFRACTION100
4.3511-46.05790.18481500.15952958X-RAY DIFFRACTION100

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