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- PDB-5d2x: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 6 ... -

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Basic information

Entry
Database: PDB / ID: 5d2x
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 6 Round5
ComponentsDe novo desinged 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 21, 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 desinged kemp eliminase KE07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4472
Polymers29,3291
Non-polymers1181
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.263, 97.263, 156.282
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-585-

HOH

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Components

#1: Protein De novo desinged 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) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.84 Å3/Da / Density % sol: 67.93 %
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: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.76→42.12 Å / Num. obs: 43891 / % possible obs: 99.89 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.1338 / Net I/σ(I): 20.64

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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: 1.76→42.116 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 2208 5.03 %
Rwork0.1928 --
obs0.1945 43888 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→42.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 8 212 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082088
X-RAY DIFFRACTIONf_angle_d1.0562829
X-RAY DIFFRACTIONf_dihedral_angle_d13.171784
X-RAY DIFFRACTIONf_chiral_restr0.042318
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.79830.35791290.31362513X-RAY DIFFRACTION98
1.7983-1.84010.27721300.2772556X-RAY DIFFRACTION100
1.8401-1.88610.32671510.26912534X-RAY DIFFRACTION100
1.8861-1.93710.32941400.26072578X-RAY DIFFRACTION100
1.9371-1.99410.26831450.23122548X-RAY DIFFRACTION100
1.9941-2.05850.24851350.2272562X-RAY DIFFRACTION100
2.0585-2.13210.26751210.21642587X-RAY DIFFRACTION100
2.1321-2.21740.26141480.2122592X-RAY DIFFRACTION100
2.2174-2.31830.24661340.21442566X-RAY DIFFRACTION100
2.3183-2.44060.25861410.20722589X-RAY DIFFRACTION100
2.4406-2.59340.24521270.20832611X-RAY DIFFRACTION100
2.5934-2.79360.2611450.20872600X-RAY DIFFRACTION100
2.7936-3.07470.24451380.19132629X-RAY DIFFRACTION100
3.0747-3.51940.20131550.17822634X-RAY DIFFRACTION100
3.5194-4.43330.16161470.14632695X-RAY DIFFRACTION100
4.4333-42.12820.18321220.1612886X-RAY DIFFRACTION100

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