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- PDB-7f1j: Designed enzyme RA61 M48K/I72D mutant: form III -

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Basic information

Entry
Database: PDB / ID: 7f1j
TitleDesigned enzyme RA61 M48K/I72D mutant: form III
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: 1.6 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
Water3,549197
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)36.032, 63.347, 39.772
Angle α, β, γ (deg.)90.000, 109.843, 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.: 197 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M tris hydrochloride, pH 8.5, 2.0 M ammonium phosphate monobasic, 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: 1.6→40 Å / Num. obs: 22093 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.1
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3543 / CC1/2: 0.674

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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: 1.6→37.41 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8812 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2132 1102 4.99 %
Rwork0.1822 20991 -
obs0.1838 22093 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 0 197 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091555
X-RAY DIFFRACTIONf_angle_d1.0362128
X-RAY DIFFRACTIONf_chiral_restr0.0699221
X-RAY DIFFRACTIONf_plane_restr0.0063271
X-RAY DIFFRACTIONf_dihedral_angle_d9.7778867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.32631370.25562610X-RAY DIFFRACTION98.78
1.67-1.760.25321330.21932598X-RAY DIFFRACTION99.89
1.76-1.870.22171420.1962629X-RAY DIFFRACTION99.75
1.87-2.020.23611360.17322616X-RAY DIFFRACTION99.53
2.02-2.220.19711380.1582618X-RAY DIFFRACTION99.46
2.22-2.540.23611380.17292621X-RAY DIFFRACTION99.75
2.54-3.20.20451370.18232630X-RAY DIFFRACTION99.68
3.2-37.410.18411410.17832669X-RAY DIFFRACTION99.08

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