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- PDB-5d2y: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 7 ... -

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Basic information

Entry
Database: PDB / ID: 5d2y
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 7 Round 5
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: 1.984 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 7 Round 5
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)29,3291
Polymers29,3291
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.877, 97.877, 156.823
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-431-

HOH

21A-507-

HOH

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Components

#1: Protein De novo designed kemp eliminase KE07


Mass: 29328.545 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.91 Å3/Da / Density % sol: 68.52 %
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: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.984→19.64 Å / Num. obs: 31217 / % possible obs: 99.51 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.1149 / Net I/σ(I): 24.47

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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: 1.984→19.639 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1574 5.04 %
Rwork0.2032 --
obs0.2046 31214 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.984→19.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 0 217 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082013
X-RAY DIFFRACTIONf_angle_d1.0422714
X-RAY DIFFRACTIONf_dihedral_angle_d12.813749
X-RAY DIFFRACTIONf_chiral_restr0.042308
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9842-2.04820.31111190.27052611X-RAY DIFFRACTION98
2.0482-2.12130.29211350.24172678X-RAY DIFFRACTION100
2.1213-2.20620.32291480.27192628X-RAY DIFFRACTION100
2.2062-2.30640.41331220.39132587X-RAY DIFFRACTION97
2.3064-2.42780.27481650.23122640X-RAY DIFFRACTION100
2.4278-2.57960.2651660.2192666X-RAY DIFFRACTION100
2.5796-2.77830.25241370.20552696X-RAY DIFFRACTION100
2.7783-3.05690.22071530.18442690X-RAY DIFFRACTION100
3.0569-3.49710.19051390.17822746X-RAY DIFFRACTION100
3.4971-4.39780.18621460.16222757X-RAY DIFFRACTION100
4.3978-19.63960.19751440.17642941X-RAY DIFFRACTION100

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