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- PDB-5ma9: GFP-binding DARPin fusion gc_R11 -

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Basic information

Entry
Database: PDB / ID: 5ma9
TitleGFP-binding DARPin fusion gc_R11
Components
  • Green fluorescent protein
  • R11
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: 1.57 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 1.0Nov 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 2.1Nov 6, 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: R11
C: R11
G: R11
E: R11
D: Green fluorescent protein
H: Green fluorescent protein
F: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,39719
Polymers237,7148
Non-polymers68311
Water37,7412095
1
B: Green fluorescent protein
A: R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6776
Polymers59,4292
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-5 kcal/mol
Surface area21320 Å2
MethodPISA
2
C: R11
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5534
Polymers59,4292
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-14 kcal/mol
Surface area21090 Å2
MethodPISA
3
G: R11
H: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6155
Polymers59,4292
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-8 kcal/mol
Surface area21320 Å2
MethodPISA
4
E: R11
F: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5534
Polymers59,4292
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-13 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.880, 89.890, 90.040
Angle α, β, γ (deg.)95.84, 116.53, 92.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Green fluorescent protein


Mass: 27453.949 Da / Num. of mol.: 4
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
R11


Mass: 31974.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2095 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.5, 30% w/v PEG 4000, 0.2 M LiSO4

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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: 1.57→44.682 Å / Num. obs: 302440 / % possible obs: 95.18 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.03
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.6 / Num. unique all: 22310 / CC1/2: 0.754 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→44.682 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2032 15124 5 %
Rwork0.1584 --
obs0.1606 302440 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→44.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16064 0 44 2095 18203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516491
X-RAY DIFFRACTIONf_angle_d0.92922354
X-RAY DIFFRACTIONf_dihedral_angle_d14.6435899
X-RAY DIFFRACTIONf_chiral_restr0.0342486
X-RAY DIFFRACTIONf_plane_restr0.0052956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5699-1.58770.31675330.24969445X-RAY DIFFRACTION94
1.5877-1.60640.28444650.2329626X-RAY DIFFRACTION95
1.6064-1.6260.28865340.22969415X-RAY DIFFRACTION95
1.626-1.64660.28445370.22389570X-RAY DIFFRACTION95
1.6466-1.66830.27384990.21199518X-RAY DIFFRACTION95
1.6683-1.69110.27295300.21049514X-RAY DIFFRACTION95
1.6911-1.71530.27835280.20129577X-RAY DIFFRACTION95
1.7153-1.74090.24484730.19469653X-RAY DIFFRACTION95
1.7409-1.76810.24555390.18379600X-RAY DIFFRACTION95
1.7681-1.79710.22335240.17649618X-RAY DIFFRACTION96
1.7971-1.82810.22055640.16719559X-RAY DIFFRACTION96
1.8281-1.86130.24034630.16889644X-RAY DIFFRACTION96
1.8613-1.89710.21764740.1719655X-RAY DIFFRACTION96
1.8971-1.93580.21755070.1639675X-RAY DIFFRACTION96
1.9358-1.97790.21675380.16659659X-RAY DIFFRACTION96
1.9779-2.02390.2115000.15949646X-RAY DIFFRACTION96
2.0239-2.07460.21645020.15729686X-RAY DIFFRACTION96
2.0746-2.13060.20665000.15369712X-RAY DIFFRACTION96
2.1306-2.19330.19884720.14859714X-RAY DIFFRACTION96
2.1933-2.26410.20745140.15239646X-RAY DIFFRACTION96
2.2641-2.34510.20945230.1489613X-RAY DIFFRACTION96
2.3451-2.43890.19335060.14639596X-RAY DIFFRACTION95
2.4389-2.54990.20484950.1479555X-RAY DIFFRACTION95
2.5499-2.68430.19154860.1479640X-RAY DIFFRACTION96
2.6843-2.85250.19674900.15539532X-RAY DIFFRACTION95
2.8525-3.07270.21474770.16389550X-RAY DIFFRACTION95
3.0727-3.38180.20544570.16069525X-RAY DIFFRACTION94
3.3818-3.87090.18494710.14699465X-RAY DIFFRACTION94
3.8709-4.8760.1514970.12739304X-RAY DIFFRACTION93
4.876-44.70050.16565260.15339404X-RAY DIFFRACTION94

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