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- PDB-9fw5: Retroaldolase 17 (RAD17) -

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Basic information

Entry
Database: PDB / ID: 9fw5
TitleRetroaldolase 17 (RAD17)
ComponentsRetroaldolase 17 (RAD17)
KeywordsDE NOVO PROTEIN / Retroaldolase / de novo enzyme / RFdiffusion
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

Downloads & links

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Assembly

Deposited unit
A: Retroaldolase 17 (RAD17)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1192
Polymers22,7041
Non-polymers4141
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-2 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.108, 107.108, 52.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Retroaldolase 17 (RAD17)


Mass: 22704.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: de novo enzyme / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-Malic acid

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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 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→53.554 Å / Num. obs: 6735 / % possible obs: 99.55 % / Redundancy: 10.4 % / Biso Wilson estimate: 25.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.89
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 645 / CC1/2: 0.525

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→53.55 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 305 4.53 %
Rwork0.2379 --
obs0.2396 6728 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→53.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 22 0 1499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111523
X-RAY DIFFRACTIONf_angle_d1.4152068
X-RAY DIFFRACTIONf_dihedral_angle_d20.371545
X-RAY DIFFRACTIONf_chiral_restr0.079249
X-RAY DIFFRACTIONf_plane_restr0.012260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.33571300.28333209X-RAY DIFFRACTION100
3.65-53.550.24271750.20633214X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5873-0.64950.24571.31740.330.3833-0.3481-0.30640.21740.05310.0506-1.0422-0.33930.35710.08980.27410.02050.12880.34690.18160.62156.1601-28.1398-18.6902
20.2450.0453-0.15240.2722-0.17350.82150.447-0.57250.26070.89860.04980.5316-0.4353-0.148-0.05070.90810.03690.43250.8682-0.00891.4368-16.1841-20.4324-12.9771
31.4141-0.43950.98060.164-0.35860.8473-0.3206-0.6217-0.21840.5514-0.0342-0.3693-0.2197-0.03-1.16570.26030.0552-0.04970.36930.17490.8033-1.4455-32.7862-15.3582
40.272-0.21620.31071.62210.37740.7592-0.17690.49110.4724-0.50540.1128-0.9298-0.31480.5129-0.62640.15450.01980.06310.20420.39440.7233-1.7682-24.4411-27.098
54.44040.596-0.5271.8538-2.05413.06810.0019-1.01990.27550.0617-0.5140.0352-0.4394-0.37390.01531.09130.006-0.08030.6276-0.30841.37495.8047-20.5502-10.251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 198 )

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