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- PDB-5ma6: GFP-binding DARPin 3G124nc -

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Basic information

Entry
Database: PDB / ID: 5ma6
TitleGFP-binding DARPin 3G124nc
Components
  • 3G124nc
  • Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel ...Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A.
CitationJournal: Sci Rep / Year: 2017
Title: Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity.
Authors: Hansen, S. / Stuber, J.C. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Pluckthun, A.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: 3G124nc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9568
Polymers44,4192
Non-polymers5376
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-43 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.310, 70.310, 432.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Green fluorescent protein


Mass: 27453.949 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 K-12 (bacteria) / References: UniProt: P42212
#2: Protein 3G124nc


Mass: 16965.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na-Acetate pH 5.5, 0.5M KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.3→50.01 Å / Num. obs: 29482 / % possible obs: 98.7 % / Redundancy: 37.3 % / CC1/2: 1 / Rmerge(I) obs: 0.148 / Net I/σ(I): 17.55
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 40.7 % / Rmerge(I) obs: 8.52 / Mean I/σ(I) obs: 0.68 / CC1/2: 0.416 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 23.158 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24096 1426 4.8 %RANDOM
Rwork0.20502 ---
obs0.20684 28037 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 29 45 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193087
X-RAY DIFFRACTIONr_bond_other_d0.0030.022923
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.9694181
X-RAY DIFFRACTIONr_angle_other_deg1.29636729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7785382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68125.616146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89915511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1871510
X-RAY DIFFRACTIONr_chiral_restr0.1480.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023504
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02682
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_it4.7645.9861537
X-RAY DIFFRACTIONr_mcbond_other4.7645.9851536
X-RAY DIFFRACTIONr_mcangle_it6.958.9691916
X-RAY DIFFRACTIONr_mcangle_other6.9498.971917
X-RAY DIFFRACTIONr_scbond_it5.5226.6241550
X-RAY DIFFRACTIONr_scbond_other5.5176.6241550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1739.7112266
X-RAY DIFFRACTIONr_long_range_B_refined12.56171.2873305
X-RAY DIFFRACTIONr_long_range_B_other12.55971.313306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 102 -
Rwork0.421 2001 -
obs--98.69 %
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)
10.8099-0.19680.11190.69010.09110.0413-0.0451-0.4322-0.1309-0.13460.0886-0.0298-0.0372-0.0908-0.04350.1846-0.01950.01360.47680.15740.05794.735927.402-7.7277
21.1916-0.4881-0.78910.5512-0.25131.6560.1008-0.0508-0.2213-0.12630.00540.1721-0.071-0.1088-0.10620.2476-0.04540.00280.2950.13560.133-12.440928.1165-29.1573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 230
2X-RAY DIFFRACTION2B10 - 168

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