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- PDB-7f1l: Designed enzyme RA61 M48K/I72D mutant: form V -

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Basic information

Entry
Database: PDB / ID: 7f1l
TitleDesigned enzyme RA61 M48K/I72D mutant: form V
ComponentsEngineered Retroaldolase
KeywordsDE NOVO PROTEIN / aldol reaction / retro-aldol reaction / mutation / reaction direction
Function / homologyIMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2923
Polymers22,1871
Non-polymers1052
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.170, 63.600, 39.170
Angle α, β, γ (deg.)90.000, 109.103, 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate trihydrate, 0.22 mM 4-hydroxy-4-(4-styrylphenyl)butan-2-one

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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 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 17348 / % possible obs: 96.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.34 Å2 / CC1/2: 0.996 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.84 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3575 / CC1/2: 0.669

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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: 1.7→37.01 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2574 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2082 861 4.97 %
Rwork0.1734 16475 -
obs0.1752 17336 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 6 130 1663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871595
X-RAY DIFFRACTIONf_angle_d1.18382174
X-RAY DIFFRACTIONf_chiral_restr0.0522222
X-RAY DIFFRACTIONf_plane_restr0.0048276
X-RAY DIFFRACTIONf_dihedral_angle_d13.0139882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.29411420.23012662X-RAY DIFFRACTION94.22
1.81-1.950.23031420.19462727X-RAY DIFFRACTION95.63
1.95-2.140.23831330.17632715X-RAY DIFFRACTION95.57
2.14-2.450.22451440.1772731X-RAY DIFFRACTION95.93
2.45-3.090.21141490.17632790X-RAY DIFFRACTION98.06
3.09-37.010.1791510.15832850X-RAY DIFFRACTION98.3

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