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- PDB-9fwa: Retroaldolase 36 (RAD36) -

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Basic information

Entry
Database: PDB / ID: 9fwa
TitleRetroaldolase 36 (RAD36)
ComponentsRetroaldolase 36 (RAD36)
KeywordsDE NOVO PROTEIN / Retroaldolase / de novo enzyme / RFdiffusion
Function / homology3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBijelic, A. / Braun, M. / Stoll, D. / Tripp, A. / Chakatok, M. / Oberdorfer, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: De novo enzyme design by artificial motif library scaffolding
Authors: Braun, M. / Tripp, A. / Stoll, D. / Kaltenbrunner, S. / Chakatok, M. / Totaro, M.G. / Hoch Cohen, S.Y. / Elaily, W. / Bijelic, A. / Hall, M. / OBerdorfer, G.
History
DepositionJun 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retroaldolase 36 (RAD36)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2324
Polymers22,9171
Non-polymers3153
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-6 kcal/mol
Surface area10070 Å2
Unit cell
Length a, b, c (Å)46.600, 55.932, 73.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Retroaldolase 36 (RAD36)


Mass: 22917.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 25% PEG3350, 0.2 M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.73→44.473 Å / Num. obs: 22076 / % possible obs: 99.86 % / Redundancy: 13.3 % / CC1/2: 0.996 / Net I/σ(I): 9.1
Reflection shellResolution: 1.73→1.792 Å / Num. unique obs: 2028 / CC1/2: 0.796

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→44.47 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1020 4.95 %
Rwork0.1885 --
obs0.1907 20607 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 20 180 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071589
X-RAY DIFFRACTIONf_angle_d0.7542143
X-RAY DIFFRACTIONf_dihedral_angle_d14.649600
X-RAY DIFFRACTIONf_chiral_restr0.04248
X-RAY DIFFRACTIONf_plane_restr0.007273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.820.33431260.2692764X-RAY DIFFRACTION100
1.82-1.940.26741270.21322772X-RAY DIFFRACTION100
1.94-2.080.25811400.20232773X-RAY DIFFRACTION100
2.08-2.290.22221530.17332762X-RAY DIFFRACTION100
2.29-2.630.21561520.18172776X-RAY DIFFRACTION100
2.63-3.310.25261580.1942793X-RAY DIFFRACTION100
3.31-44.470.20621640.17662947X-RAY DIFFRACTION100

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