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- PDB-8sfx: High Affinity nanobodies against GFP -

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Basic information

Entry
Database: PDB / ID: 8sfx
TitleHigh Affinity nanobodies against GFP
Components
  • Green fluorescent protein
  • LaG21
KeywordsIMMUNE SYSTEM / Nanobody / nanobodies / GFP / green fluorescent protein / high-affinity antibody variant / antibody variant / single-domain antibody
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / D-MALATE / PHOSPHATE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKetaren, N.E. / Rout, M.P. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2025
Title: Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies.
Authors: Ketaren, N.E. / Fridy, P.C. / Malashkevich, V. / Sanyal, T. / Brillantes, M. / Thompson, M.K. / Oren, D.A. / Bonanno, J.B. / Sali, A. / Almo, S.C. / Chait, B.T. / Rout, M.P.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Green fluorescent protein
D: LaG21
C: LaG21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,35937
Polymers88,5294
Non-polymers1,83033
Water2,630146
1
A: Green fluorescent protein
C: LaG21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,12116
Polymers44,2652
Non-polymers85614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-88 kcal/mol
Surface area15620 Å2
MethodPISA
2
B: Green fluorescent protein
D: LaG21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,23921
Polymers44,2652
Non-polymers97419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-125 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.122, 111.122, 194.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-307-

NA

21B-308-

NA

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Green fluorescent protein


Mass: 28794.396 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 LaG21


Mass: 15470.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 179 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1 M bis-tris propane pH 7.0, 1.2 M DL-malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 85311 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 1.403 / Mean I/σ(I) obs: 2 / Num. unique obs: 12451 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALAdata scaling
MOSFLM6.2.3data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→36.67 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1991 2.47 %
Rwork0.2101 --
obs0.2106 80508 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 102 146 5688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125628
X-RAY DIFFRACTIONf_angle_d1.1077609
X-RAY DIFFRACTIONf_dihedral_angle_d9.772774
X-RAY DIFFRACTIONf_chiral_restr0.117809
X-RAY DIFFRACTIONf_plane_restr0.011991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.37261190.34634778X-RAY DIFFRACTION81
2-2.050.31321330.32815088X-RAY DIFFRACTION86
2.05-2.110.32781310.30075271X-RAY DIFFRACTION89
2.11-2.180.32631390.28955469X-RAY DIFFRACTION92
2.18-2.260.26231390.26095444X-RAY DIFFRACTION92
2.26-2.350.29471440.25985538X-RAY DIFFRACTION94
2.35-2.460.23831500.24275654X-RAY DIFFRACTION95
2.46-2.590.28641410.25415749X-RAY DIFFRACTION97
2.59-2.750.29271480.24655848X-RAY DIFFRACTION98
2.75-2.960.30231460.25965861X-RAY DIFFRACTION99
2.96-3.260.24561440.22245942X-RAY DIFFRACTION100
3.26-3.730.21311530.20195940X-RAY DIFFRACTION100
3.73-4.70.16071530.15175950X-RAY DIFFRACTION100
4.7-36.670.17571510.16065985X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -27.8072 Å / Origin y: -10.3191 Å / Origin z: 5.773 Å
111213212223313233
T0.2436 Å20.0003 Å2-0.0039 Å2-0.4637 Å20.0011 Å2--0.3489 Å2
L0.0172 °2-0.0056 °2-0.4435 °2-0.2474 °20.0047 °2--0.5045 °2
S-0.183 Å °0.0084 Å °-0.0745 Å °0.0031 Å °-0.017 Å °0.0008 Å °0.2435 Å °-0.002 Å °0.1909 Å °
Refinement TLS groupSelection details: all

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