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- PDB-7f1k: Designed enzyme RA61 M48K/I72D mutant: form IV -

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Basic information

Entry
Database: PDB / ID: 7f1k
TitleDesigned enzyme RA61 M48K/I72D mutant: form IV
ComponentsEngineered Retroaldolase
KeywordsDE NOVO PROTEIN / aldol reaction / retro-aldol reaction / mutation / reaction direction
Function / homologyGlycoside hydrolase family 11/12, catalytic domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsFujioka, T. / Oka, M. / Numoto, N. / Ito, N. / Oda, M. / Tanaka, F.
CitationJournal: Chembiochem / Year: 2022
Title: Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions.
Authors: Fujioka, T. / Numoto, N. / Akama, H. / Shilpa, K. / Oka, M. / Roy, P.K. / Krishna, Y. / Ito, N. / Baker, D. / Oda, M. / Tanaka, F.
History
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered Retroaldolase


Theoretical massNumber of molelcules
Total (without water)22,1871
Polymers22,1871
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.226, 36.805, 37.544
Angle α, β, γ (deg.)111.987, 96.507, 109.191
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Engineered Retroaldolase


Mass: 22187.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.74 Å3/Da / Density % sol: 29.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M trisodium citrate dihydrate, pH 5.6, 20% (v/v) 2-propanol, 20% (w/v) PEG4000, 1.7 mM ethyl 6,6,6-trifluoro-5-hydroxy-3-oxo-5-phenyl-hexanoate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→20 Å / Num. obs: 64002 / % possible obs: 91.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 1 / Net I/σ(I): 17.1
Reflection shellResolution: 1.05→1.11 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9596 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B5L

3b5l


Resolution: 1.05→17.58 Å / SU ML: 0.1181 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.2473 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1717 3198 5.01 %
Rwork0.1512 60692 -
obs0.1523 63890 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.44 Å2
Refinement stepCycle: LAST / Resolution: 1.05→17.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 0 215 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511682
X-RAY DIFFRACTIONf_angle_d0.9642311
X-RAY DIFFRACTIONf_chiral_restr0.0803239
X-RAY DIFFRACTIONf_plane_restr0.0049296
X-RAY DIFFRACTIONf_dihedral_angle_d13.5104590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.37291130.36552265X-RAY DIFFRACTION78.59
1.07-1.080.33751370.30962471X-RAY DIFFRACTION85.9
1.08-1.10.30221310.27422514X-RAY DIFFRACTION85.88
1.1-1.120.27431360.24872473X-RAY DIFFRACTION87.46
1.12-1.140.24351510.23262521X-RAY DIFFRACTION87.49
1.14-1.160.26451180.21352581X-RAY DIFFRACTION88.58
1.16-1.190.21511430.20892624X-RAY DIFFRACTION90.42
1.19-1.210.23671230.19812604X-RAY DIFFRACTION90.33
1.21-1.240.21991330.18662599X-RAY DIFFRACTION90.14
1.24-1.270.26151460.1822646X-RAY DIFFRACTION91
1.27-1.30.23221360.17772624X-RAY DIFFRACTION91.76
1.3-1.340.21531520.16412668X-RAY DIFFRACTION91.92
1.34-1.390.18681500.15732665X-RAY DIFFRACTION92.54
1.39-1.440.20881410.14592681X-RAY DIFFRACTION92.92
1.44-1.490.20031260.14212714X-RAY DIFFRACTION93.76
1.49-1.560.1491320.13272721X-RAY DIFFRACTION93.73
1.56-1.640.16251470.1342695X-RAY DIFFRACTION94.61
1.64-1.750.17321700.14462740X-RAY DIFFRACTION94.48
1.75-1.880.17331460.14112707X-RAY DIFFRACTION94.72
1.88-2.070.14751210.12952781X-RAY DIFFRACTION95.02
2.07-2.370.19161480.14042782X-RAY DIFFRACTION96.32
2.37-2.980.14311630.1492792X-RAY DIFFRACTION97.52
2.98-17.580.12761350.12952824X-RAY DIFFRACTION97.18

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