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- PDB-9f24: DARPin eGFP complex DP4 (2G71) -

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Basic information

Entry
Database: PDB / ID: 9f24
TitleDARPin eGFP complex DP4 (2G71)
Components
  • DARPin DP4
  • 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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsMittl, P.R. / Winkelvoss, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: DARPin eGFP complex DP4 (2G71)
Authors: Winkelvoss, D. / Pluckthun, A.
History
DepositionApr 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
C: DARPin DP4


Theoretical massNumber of molelcules
Total (without water)40,1502
Polymers40,1502
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.026, 136.026, 75.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Green fluorescent protein


Mass: 27100.576 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 DP4


Mass: 13049.582 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 8.5, 8% PEG 20000, 8% PEG 550 MME, 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: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.057→43.02 Å / Num. obs: 42465 / % possible obs: 98.8 % / Redundancy: 8.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.086 / Net I/σ(I): 10.75
Reflection shellResolution: 2.057→2.18 Å / Num. unique obs: 6598 / CC1/2: 0.421

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→43.02 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.75 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22156 2129 5 %RANDOM
Rwork0.18222 ---
obs0.18414 40447 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.06→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 0 261 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162672
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.6533861
X-RAY DIFFRACTIONr_angle_other_deg0.5651.5896168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.896516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29510485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
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_it2.8152.7521423
X-RAY DIFFRACTIONr_mcbond_other2.8012.7521423
X-RAY DIFFRACTIONr_mcangle_it3.9544.9231777
X-RAY DIFFRACTIONr_mcangle_other3.9544.9241778
X-RAY DIFFRACTIONr_scbond_it3.8643.1031428
X-RAY DIFFRACTIONr_scbond_other3.8633.1041429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7955.5262085
X-RAY DIFFRACTIONr_long_range_B_refined8.98927.423097
X-RAY DIFFRACTIONr_long_range_B_other8.96626.093045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.11 Å
RfactorNum. reflection% reflection
Rfree0.457 149 -
Rwork0.453 2845 -
obs--95.5 %
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)
12.9305-0.0730.6982.2601-0.65862.8137-0.0748-0.1603-0.0432-0.01190.00220.07760.3315-0.37210.07250.2408-0.10620.03860.2461-0.01480.0107-25.196841.5719-0.4018
22.1260.1865-0.07533.71220.16592.4867-0.00260.12040.1798-0.2023-0.0781-0.0614-0.0008-0.19990.08070.2056-0.04380.01080.21940.02070.0425-23.091155.1202-24.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 234
2X-RAY DIFFRACTION2C12 - 134

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