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- PDB-5d30: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 9 ... -

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Basic information

Entry
Database: PDB / ID: 5d30
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 9 Round 5
ComponentsDe novo kemp eliminase KE07 round 5
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: 1.69 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 9 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 / 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 5


Theoretical massNumber of molelcules
Total (without water)29,3291
Polymers29,3291
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.802, 96.802, 155.413
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 kemp eliminase KE07 round 5


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.: 242 / 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: 3.79 Å3/Da / Density % sol: 67.53 %
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: 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: 1.69→41.92 Å / Num. obs: 48768 / % possible obs: 99.99 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.1255 / Net I/σ(I): 17.38

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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: 1.69→41.916 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 2466 5.06 %
Rwork0.1834 --
obs0.1851 48765 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→41.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 242 2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172060
X-RAY DIFFRACTIONf_angle_d1.6882788
X-RAY DIFFRACTIONf_dihedral_angle_d13.464767
X-RAY DIFFRACTIONf_chiral_restr0.096314
X-RAY DIFFRACTIONf_plane_restr0.009362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.72250.31811340.29522523X-RAY DIFFRACTION100
1.7225-1.75770.30651340.26852512X-RAY DIFFRACTION100
1.7577-1.79590.25941410.24682529X-RAY DIFFRACTION100
1.7959-1.83770.24521220.22432517X-RAY DIFFRACTION100
1.8377-1.88360.22251570.23382527X-RAY DIFFRACTION100
1.8836-1.93460.32171290.24012528X-RAY DIFFRACTION100
1.9346-1.99150.28531580.21152504X-RAY DIFFRACTION100
1.9915-2.05580.22221350.21582546X-RAY DIFFRACTION100
2.0558-2.12930.23911350.19992543X-RAY DIFFRACTION100
2.1293-2.21450.25251390.18942550X-RAY DIFFRACTION100
2.2145-2.31530.23921340.18632554X-RAY DIFFRACTION100
2.3153-2.43730.20981200.18982579X-RAY DIFFRACTION100
2.4373-2.590.22211310.1912565X-RAY DIFFRACTION100
2.59-2.790.23381530.19392579X-RAY DIFFRACTION100
2.79-3.07070.21811330.18092589X-RAY DIFFRACTION100
3.0707-3.51480.22131440.1762629X-RAY DIFFRACTION100
3.5148-4.42750.17151390.14572670X-RAY DIFFRACTION100
4.4275-41.92940.15881280.15172855X-RAY DIFFRACTION100

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