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- PDB-9gbt: De novo designed retro-aldolase 13 (RAD13) -

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Basic information

Entry
Database: PDB / ID: 9gbt
TitleDe novo designed retro-aldolase 13 (RAD13)
ComponentsRetroaldolase 13 (RAD13)
KeywordsDE NOVO PROTEIN / Retroaldolase / de novo enzyme / RFdiffusion
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsBijelic, A. / Stoll, D. / Chakatok, M. / Tripp, A. / Braun, M. / Oberdorfer, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: Computational design of highly active de novo enzymes
Authors: Braun, M. / Tripp, A. / Chakatok, M. / Kaltenbrunner, S. / Stoll, D. / Bijelic, A. / Wael, E. / Totaro, M.G. / Hoch, S.Y. / Hall, M. / Aleotti, M. / Oberdorfer, G.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retroaldolase 13 (RAD13)
B: Retroaldolase 13 (RAD13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,66212
Polymers44,9432
Non-polymers72010
Water45025
1
A: Retroaldolase 13 (RAD13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9488
Polymers22,4711
Non-polymers4767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retroaldolase 13 (RAD13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7154
Polymers22,4711
Non-polymers2433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.044, 76.936, 59.619
Angle α, β, γ (deg.)90.000, 91.234, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 85 or resid 87 through 200))
d_2ens_1(chain "B" and (resid 1 through 85 or resid 87 through 200))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYALAALAAA1 - 852 - 86
d_12LYSLYSPHEPHEAA87 - 20088 - 201
d_21GLYGLYALAALABB1 - 852 - 86
d_22LYSLYSPHEPHEBB87 - 20088 - 201

NCS oper: (Code: givenMatrix: (0.999836815295, -0.0166435039214, 0.00702399867744), (-0.0168496318357, -0.999396225433, 0.0303854323253), (0.00651403770362, -0.0304988256792, -0.999513576168)Vector: ...NCS oper: (Code: given
Matrix: (0.999836815295, -0.0166435039214, 0.00702399867744), (-0.0168496318357, -0.999396225433, 0.0303854323253), (0.00651403770362, -0.0304988256792, -0.999513576168)
Vector: 17.5251282934, -13.7520523627, 31.9840051819)

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Components

#1: Protein Retroaldolase 13 (RAD13)


Mass: 22471.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.94 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Hampton Research JCSG Plus A1 50% PEG 400, 0.1 M Sodium acetate pH 4.5

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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: Apr 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.428→59.61 Å / Num. obs: 15039 / % possible obs: 98.94 % / Redundancy: 7.2 % / Biso Wilson estimate: 57.89 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.08844 / Rrim(I) all: 0.2384 / Net I/σ(I): 4.54
Reflection shellResolution: 2.43→2.62 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.641 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 2922 / CC1/2: 0.46 / CC star: 0.794 / Rpim(I) all: 1.081 / Rrim(I) all: 2.859 / % possible all: 98.88

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→59.61 Å / SU ML: 0.4502 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.7971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 652 5.04 %
Rwork0.223 12288 -
obs0.2255 12940 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.79 Å2
Refinement stepCycle: LAST / Resolution: 2.43→59.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 47 25 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273202
X-RAY DIFFRACTIONf_angle_d0.52614266
X-RAY DIFFRACTIONf_chiral_restr0.0326465
X-RAY DIFFRACTIONf_plane_restr0.0045558
X-RAY DIFFRACTIONf_dihedral_angle_d14.12981261
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.984386804657 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.620.35051280.32952438X-RAY DIFFRACTION98.88
2.62-2.880.35621380.27132454X-RAY DIFFRACTION99.39
2.88-3.30.35241110.23682488X-RAY DIFFRACTION99.62
3.3-4.150.22521260.20082466X-RAY DIFFRACTION99.23
4.15-59.610.25041490.20732442X-RAY DIFFRACTION97.63

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