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- PDB-9fw7: Retroaldolase 32 (RAD32) -

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Basic information

Entry
Database: PDB / ID: 9fw7
TitleRetroaldolase 32 (RAD32)
ComponentsRetroaldolase 32 (RAD32)
KeywordsDE NOVO PROTEIN / Retroaldolase / de novo enzyme / RFdiffusion
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. / 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

Downloads & links

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Assembly

Deposited unit
A: Retroaldolase 32 (RAD32)


Theoretical massNumber of molelcules
Total (without water)22,9221
Polymers22,9221
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9080 Å2
Unit cell
Length a, b, c (Å)60.510, 60.510, 41.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Retroaldolase 32 (RAD32)


Mass: 22922.451 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M MIB (sodium malonate dibasic monohydrate, imidazole, and boric acid), 15% PEG1500

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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: 2→32.45 Å / Num. obs: 15322 / % possible obs: 99.89 % / Redundancy: 10.8 % / CC1/2: 0.996 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.2 Å / Num. unique obs: 3822 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.45 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 572 5.01 %
Rwork0.2162 --
obs0.2191 11427 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 39 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021524
X-RAY DIFFRACTIONf_angle_d0.5172065
X-RAY DIFFRACTIONf_dihedral_angle_d19.422559
X-RAY DIFFRACTIONf_chiral_restr0.034248
X-RAY DIFFRACTIONf_plane_restr0.003261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.33761440.25952722X-RAY DIFFRACTION100
2.2-2.520.28971430.2262718X-RAY DIFFRACTION100
2.52-3.170.29951430.23662719X-RAY DIFFRACTION100
3.18-32.450.24391420.19692696X-RAY DIFFRACTION100

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