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- PDB-7f1h: Designed enzyme RA61 M48K/I72D mutant: form I -

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Basic information

Entry
Database: PDB / ID: 7f1h
TitleDesigned enzyme RA61 M48K/I72D mutant: form I
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 / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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

Downloads & links

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Assembly

Deposited unit
A: Engineered Retroaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5097
Polymers22,1871
Non-polymers3226
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.644, 64.236, 42.682
Angle α, β, γ (deg.)90.000, 111.074, 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: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 40.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M HEPES, pH 7.5, 2.0 M ammonium formate, 8.6 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: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.14→40 Å / Num. obs: 60111 / % possible obs: 90.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 8.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 1.14→1.2 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5336 / CC1/2: 0.947

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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: 1.14→39.83 Å / SU ML: 0.0761 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.9973 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1469 3013 5.01 %
Rwork0.1244 57090 -
obs0.1256 60103 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.11 Å2
Refinement stepCycle: LAST / Resolution: 1.14→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 21 294 1805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451573
X-RAY DIFFRACTIONf_angle_d0.93952141
X-RAY DIFFRACTIONf_chiral_restr0.0836220
X-RAY DIFFRACTIONf_plane_restr0.0057269
X-RAY DIFFRACTIONf_dihedral_angle_d13.4253530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.2551300.179713X-RAY DIFFRACTION24.65
1.15-1.170.1767840.16391430X-RAY DIFFRACTION51.03
1.17-1.190.1643890.14391786X-RAY DIFFRACTION62.69
1.19-1.210.21561090.13772119X-RAY DIFFRACTION74.29
1.21-1.240.17061430.13982621X-RAY DIFFRACTION92.32
1.24-1.260.16481460.1312835X-RAY DIFFRACTION99.43
1.26-1.290.15311540.1242841X-RAY DIFFRACTION99.77
1.29-1.320.17171430.11362840X-RAY DIFFRACTION99.67
1.32-1.350.14971630.11712836X-RAY DIFFRACTION99.87
1.35-1.390.13011340.11272830X-RAY DIFFRACTION99.9
1.39-1.430.13531520.10982876X-RAY DIFFRACTION99.67
1.43-1.480.15231510.10922827X-RAY DIFFRACTION99.93
1.48-1.530.13981670.10592844X-RAY DIFFRACTION99.83
1.53-1.590.12531370.10412827X-RAY DIFFRACTION99.63
1.59-1.660.1361620.10512853X-RAY DIFFRACTION99.83
1.66-1.750.14591400.11082853X-RAY DIFFRACTION99.7
1.75-1.860.13161590.11782854X-RAY DIFFRACTION99.57
1.86-20.12591440.11292820X-RAY DIFFRACTION99.13
2-2.210.14741530.11442855X-RAY DIFFRACTION99.73
2.21-2.520.13811540.13232875X-RAY DIFFRACTION99.67
2.52-3.180.17621400.1442860X-RAY DIFFRACTION99.44
3.18-39.830.13851590.13462895X-RAY DIFFRACTION99.12

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