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- PDB-7f1i: Designed enzyme RA61 M48K/I72D mutant: form II -

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Basic information

Entry
Database: PDB / ID: 7f1i
TitleDesigned enzyme RA61 M48K/I72D mutant: form II
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: 1.4 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
Water3,369187
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)36.112, 63.428, 43.186
Angle α, β, γ (deg.)90.000, 112.133, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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.: 187 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium cacodylate trihydrate, pH 6.5, 1.4 M sodium acetate trihydrate, 2 mM acetylacetone

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 35272 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 1.4→1.49 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5654 / CC1/2: 0.823

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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: 1.4→40 Å / SU ML: 0.147 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5226 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2036 1768 5.02 %
Rwork0.1819 33472 -
obs0.183 35240 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 0 187 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591557
X-RAY DIFFRACTIONf_angle_d0.90732129
X-RAY DIFFRACTIONf_chiral_restr0.0828220
X-RAY DIFFRACTIONf_plane_restr0.0049270
X-RAY DIFFRACTIONf_dihedral_angle_d14.703524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.36561400.32332536X-RAY DIFFRACTION98.2
1.44-1.480.29691310.28892553X-RAY DIFFRACTION99.67
1.48-1.530.27831370.25672585X-RAY DIFFRACTION99.93
1.53-1.580.27131320.23722578X-RAY DIFFRACTION99.63
1.58-1.650.27031390.21982582X-RAY DIFFRACTION99.71
1.65-1.720.24831360.20732590X-RAY DIFFRACTION99.89
1.72-1.810.22531320.20362564X-RAY DIFFRACTION99.93
1.81-1.930.23391410.19382562X-RAY DIFFRACTION99.59
1.93-2.080.18551360.17432576X-RAY DIFFRACTION99.52
2.08-2.280.21411390.17382579X-RAY DIFFRACTION99.16
2.28-2.610.19791350.17612572X-RAY DIFFRACTION99.52
2.61-3.290.19471290.17662604X-RAY DIFFRACTION99.17
3.29-400.15561410.14442591X-RAY DIFFRACTION98.41

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