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- PDB-5ma4: GFP-binding DARPin fusion gc_K7 -

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Basic information

Entry
Database: PDB / ID: 5ma4
TitleGFP-binding DARPin fusion gc_K7
Components
  • Green fluorescent protein
  • K7
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
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 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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 / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Green fluorescent protein
A: K7


Theoretical massNumber of molelcules
Total (without water)58,8172
Polymers58,8172
Non-polymers00
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-13 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.880, 92.340, 56.530
Angle α, β, γ (deg.)90.00, 114.60, 90.00
Int Tables number4
Space group name H-MP1211

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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 K7


Mass: 31362.932 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.: 725 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium Acetate trihydrate, 0.1M TRIS HCl pH 8.5, 30%w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→47.293 Å / Num. obs: 102263 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.63
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.11 / CC1/2: 0.735 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.293 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 4853 4.75 %
Rwork0.1418 --
obs0.1432 102235 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 0 725 4757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144403
X-RAY DIFFRACTIONf_angle_d1.2756019
X-RAY DIFFRACTIONf_dihedral_angle_d18.1321604
X-RAY DIFFRACTIONf_chiral_restr0.096663
X-RAY DIFFRACTIONf_plane_restr0.009811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.26861780.24453209X-RAY DIFFRACTION100
1.4159-1.43260.26691390.2233242X-RAY DIFFRACTION100
1.4326-1.450.24831670.21443233X-RAY DIFFRACTION100
1.45-1.46840.26651680.20083206X-RAY DIFFRACTION100
1.4684-1.48770.20781820.18053234X-RAY DIFFRACTION100
1.4877-1.50810.21591460.17123247X-RAY DIFFRACTION100
1.5081-1.52960.2021670.16383227X-RAY DIFFRACTION100
1.5296-1.55250.19761770.15963234X-RAY DIFFRACTION100
1.5525-1.57670.20171730.15333198X-RAY DIFFRACTION100
1.5767-1.60260.19921690.15033242X-RAY DIFFRACTION100
1.6026-1.63020.19611430.14383252X-RAY DIFFRACTION100
1.6302-1.65990.17241470.14583278X-RAY DIFFRACTION100
1.6599-1.69180.18121600.13813261X-RAY DIFFRACTION100
1.6918-1.72630.1471600.12963218X-RAY DIFFRACTION100
1.7263-1.76390.19291640.13163234X-RAY DIFFRACTION100
1.7639-1.80490.16231410.12953284X-RAY DIFFRACTION100
1.8049-1.850.17741620.12643215X-RAY DIFFRACTION100
1.85-1.90.17011570.13473261X-RAY DIFFRACTION100
1.9-1.9560.16831950.13043233X-RAY DIFFRACTION100
1.956-2.01910.17321350.13853276X-RAY DIFFRACTION100
2.0191-2.09130.16861620.13553246X-RAY DIFFRACTION100
2.0913-2.1750.18551690.13643251X-RAY DIFFRACTION100
2.175-2.2740.15721590.13713228X-RAY DIFFRACTION100
2.274-2.39390.16651600.13063251X-RAY DIFFRACTION100
2.3939-2.54380.15422180.12843216X-RAY DIFFRACTION100
2.5438-2.74020.19381650.13773226X-RAY DIFFRACTION100
2.7402-3.01590.15141420.14413297X-RAY DIFFRACTION100
3.0159-3.45220.15872050.14463213X-RAY DIFFRACTION100
3.4522-4.3490.1309950.12383346X-RAY DIFFRACTION100
4.349-47.31980.16241480.15423324X-RAY DIFFRACTION100

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