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- PDB-9f23: DARPin eGFP complex DP2 (2G156) -

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Basic information

Entry
Database: PDB / ID: 9f23
TitleDARPin eGFP complex DP2 (2G156)
Components
  • DARPin DP2
  • 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 / : / Chem-PXN / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMittl, P.R. / Hansen, S.
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 DP2
C: Green fluorescent protein
D: DARPin DP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,72830
Polymers82,0294
Non-polymers2,69926
Water13,403744
1
A: Green fluorescent protein
B: DARPin DP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,14914
Polymers41,0142
Non-polymers1,13412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Green fluorescent protein
D: DARPin DP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,57916
Polymers41,0142
Non-polymers1,56514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.870, 95.160, 69.470
Angle α, β, γ (deg.)90.00, 115.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Green fluorescent protein


Mass: 27453.949 Da / Num. of mol.: 2
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 DP2


Mass: 13560.381 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)

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Non-polymers , 6 types, 770 molecules

#3: Chemical ChemComp-A1H87 / 2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]methyl]propane-1,3-diol


Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O8
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 50%pentaerythriol propoxylate 0.1 M Tris, pH 8.0

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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: Sep 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→48.08 Å / Num. obs: 95818 / % possible obs: 98.63 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Net I/σ(I): 14.1
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 3412 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→48.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.669 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21167 4677 4.9 %RANDOM
Rwork0.17363 ---
obs0.17551 91261 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.534 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å2-0.47 Å2
2--3 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.59→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 0 177 744 6426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126253
X-RAY DIFFRACTIONr_bond_other_d0.0050.0165795
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6588498
X-RAY DIFFRACTIONr_angle_other_deg0.5071.59313570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.887522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.538101076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027150
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021122
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_it0.6290.5473076
X-RAY DIFFRACTIONr_mcbond_other0.6150.5423070
X-RAY DIFFRACTIONr_mcangle_it1.0290.83912
X-RAY DIFFRACTIONr_mcangle_other1.0310.8013913
X-RAY DIFFRACTIONr_scbond_it1.3450.7893177
X-RAY DIFFRACTIONr_scbond_other1.3450.7893178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8921.0954587
X-RAY DIFFRACTIONr_long_range_B_refined7.08417.8766958
X-RAY DIFFRACTIONr_long_range_B_other6.93211.4526728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 337 -
Rwork0.34 6473 -
obs--95.13 %
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)
11.68070.0001-0.1511.2106-0.06341.4350.02350.12950.0103-0.006-0.01540.00790.00060.0939-0.00810.0862-0.0026-0.01150.0818-0.00690.0603-59.7127-3.107624.4118
22.8655-0.27080.9090.9097-0.19132.6703-0.0112-0.09160.11490.0214-0.01220.0874-0.1613-0.18320.02340.10610.00550.00390.09840.00310.0875-83.13433.299535.8292
31.49260.0315-0.07451.22510.04141.33340.0218-0.079-0.0014-0.0067-0.0231-0.0036-0.0286-0.0840.00120.0896-0.0006-0.01720.01030.00050.0615-98.3062-3.07081.0183
42.76560.29070.50860.93210.11142.3723-0.0090.14310.11510.01190.0037-0.0914-0.19480.22360.00530.1132-0.02030.00010.1169-0.00210.0925-74.94753.4489-10.4013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 230
2X-RAY DIFFRACTION2B12 - 136
3X-RAY DIFFRACTION3C1 - 230
4X-RAY DIFFRACTION4D13 - 136

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