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- PDB-9f22: DARPin eGFP complex DP1 (3G190.24) -

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Basic information

Entry
Database: PDB / ID: 9f22
TitleDARPin eGFP complex DP1 (3G190.24)
Components
  • DARPin DP1
  • Green fluorescent protein
KeywordsPROTEIN BINDING / DARPin / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / BROMIDE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMittl, P.R. / Winkelvoss, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Commun Biol / Year: 2025
Title: Molecular features defining the efficiency of bioPROTACs.
Authors: Winkelvoss, D. / Vukovic, D. / Hanny, A.C. / Riermeier, L. / Udovcic, A. / Kolibius, J. / Honegger, A. / Mittl, P.R.E. / Michel, E. / Hansen, S. / Pluckthun, A.
History
DepositionApr 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: DARPin DP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9945
Polymers43,7902
Non-polymers2043
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint1 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.039, 77.039, 152.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Green fluorescent protein


Mass: 27130.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Protein DARPin DP1


Mass: 16659.582 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)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na acetate pH 5.5, 10% e/v PEG 8K, 10% PEG 1K, 0.2 M KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40.5 Å / Num. obs: 20210127 / % possible obs: 99.62 % / Redundancy: 9.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.066 / Rrim(I) all: 0.207 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2676 / CC1/2: 0.415 / Rpim(I) all: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.909 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22292 1397 5.1 %RANDOM
Rwork0.1741 ---
obs0.17663 25816 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 9 156 3163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123094
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162810
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.6484195
X-RAY DIFFRACTIONr_angle_other_deg0.4561.5786556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5075386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.28512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35110520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023517
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02571
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0144.0091544
X-RAY DIFFRACTIONr_mcbond_other3.0134.0091544
X-RAY DIFFRACTIONr_mcangle_it4.21161930
X-RAY DIFFRACTIONr_mcangle_other4.2136.0011931
X-RAY DIFFRACTIONr_scbond_it4.2294.5451550
X-RAY DIFFRACTIONr_scbond_other4.2284.5451549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6616.6032266
X-RAY DIFFRACTIONr_long_range_B_refined8.65455.3933282
X-RAY DIFFRACTIONr_long_range_B_other8.63655.1573254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 113 -
Rwork0.305 1847 -
obs--99.39 %
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)
13.192-0.2828-0.67232.90670.19932.65190.1136-0.16620.11560.1766-0.02720.2332-0.0181-0.1561-0.08630.0172-0.00120.02280.07250.01550.03471.724-21.977715.5464
23.1786-0.78410.84373.4608-1.76453.76950.0817-0.02140.1324-0.1096-0.00010.0304-0.04030.0595-0.08160.0164-0.00580.00930.0027-0.00460.011826.9896-20.17093.5935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 302
2X-RAY DIFFRACTION2B2 - 156

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