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

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Basic information

Entry
Database: PDB / ID: 8sfz
TitleHigh Affinity nanobodies against GFP
Components
  • (Green fluorescent ...) x 2
  • LaG35
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 / : / Green fluorescent protein
Function and homology information
Biological speciesLama glama (llama)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: To Be Published
Title: High Affinity nanobodies against GFP
Authors: Ketaren, N.E. / Rout, M.P. / Almo, S.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: LaG35
A: LaG35
B: LaG35
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,67711
Polymers134,5136
Non-polymers1635
Water7,314406
1
C: LaG35
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8854
Polymers44,8232
Non-polymers622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LaG35
F: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8854
Polymers44,8232
Non-polymers622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: LaG35
E: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9063
Polymers44,8672
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.649, 101.731, 184.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11F-301-

K

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Components

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Green fluorescent ... , 2 types, 3 molecules DFE

#2: 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
#3: Protein Green fluorescent protein /


Mass: 28838.451 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

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Antibody , 1 types, 3 molecules CAB

#1: Antibody LaG35


Mass: 16028.683 Da / Num. of mol.: 3
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 , 3 types, 411 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium formate pH 7.3, 20% (w/v) PEG335

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 107233 / % possible obs: 89.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Χ2: 2.741 / Net I/σ(I): 9.4 / Num. measured all: 212023
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.931.70.27233993.558157.9
1.97-2.0120.46859411.222199.9
2.01-2.0520.40359581.241199.8
2.05-2.0920.34359191.431199.7
2.09-2.1420.29760001.6199.8
2.14-2.1920.2959211.6199.6
2.19-2.251.80.33231442.195152.7
2.25-2.321.90.28333002.062155.3
2.32-2.3920.1959442.041199.4
2.39-2.4820.15959232.151199
2.48-2.5820.1458922.457199.1
2.58-2.720.12758612.634198.5
2.7-2.8420.11158883.138198.3
2.84-3.0220.09658593.478198.3
3.02-3.251.90.08157884.186197.7
3.25-3.581.90.07258354.823196.8
3.58-4.091.80.06632696.085154.9
4.09-5.161.80.05556835.775195.1
5.16-5020.04957255.105195.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.1 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1999 1.94 %
Rwork0.2066 --
obs0.2071 103243 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8341 0 5 406 8752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128535
X-RAY DIFFRACTIONf_angle_d1.07511544
X-RAY DIFFRACTIONf_dihedral_angle_d8.1941156
X-RAY DIFFRACTIONf_chiral_restr0.0611229
X-RAY DIFFRACTIONf_plane_restr0.0091502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.38421320.34926701X-RAY DIFFRACTION93
1.95-20.28881400.29867105X-RAY DIFFRACTION99
2-2.060.30971420.277193X-RAY DIFFRACTION100
2.06-2.130.30791420.25627214X-RAY DIFFRACTION100
2.13-2.20.261430.24657199X-RAY DIFFRACTION100
2.2-2.290.32351430.2747221X-RAY DIFFRACTION100
2.29-2.390.33211430.24437234X-RAY DIFFRACTION100
2.39-2.520.26971420.23567239X-RAY DIFFRACTION100
2.52-2.680.29621440.23147286X-RAY DIFFRACTION100
2.68-2.880.28991440.22857255X-RAY DIFFRACTION100
2.88-3.170.27651440.22337303X-RAY DIFFRACTION100
3.17-3.630.2161450.19937352X-RAY DIFFRACTION100
3.63-4.580.16621460.16067367X-RAY DIFFRACTION100
4.58-46.10.18281490.17397575X-RAY DIFFRACTION99

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