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- PDB-7sah: Crystal Structure of LaG16 Nanobody bound to eGFP -

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Basic information

Entry
Database: PDB / ID: 7sah
TitleCrystal Structure of LaG16 Nanobody bound to eGFP
Components
  • Green fluorescent protein
  • LaG16
KeywordsIMMUNE SYSTEM / Antibody / nanobody / affinity tag / fluorescent protein
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 speciesAequorea victoria (jellyfish)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCong, A.T.Q. / Schellenberg, M.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Protein Sci. / Year: 2022
Title: High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices.
Authors: Cong, A.T.Q. / Witter, T.L. / Schellenberg, M.J.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: LaG16


Theoretical massNumber of molelcules
Total (without water)42,9982
Polymers42,9982
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.353, 88.238, 132.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-530-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 26882.299 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
#2: Antibody LaG16


Mass: 16115.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100mM BICINE with 2% (w/v) 1,4-Dioxane and 10% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 58133 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 1.039 / Net I/σ(I): 11.9 / Num. measured all: 393519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.665.71.05457500.5440.4761.160.95699.7
1.66-1.7270.76557000.7850.3120.8270.999100
1.72-1.87.10.53457770.8810.2160.5771.062100
1.8-1.96.90.34957550.9490.1430.3781.091100
1.9-2.026.60.20357700.980.0850.221.078100
2.02-2.176.80.13257950.9910.0540.1431.064100
2.17-2.397.20.09458000.9950.0380.1011.049100
2.39-2.746.90.06258330.9980.0260.0671.054100
2.74-3.456.70.03858800.9990.0150.0410.955100
3.45-506.80.02860730.9990.0110.031.06100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUL

4eul


Resolution: 1.6→44.12 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 1992 3.43 %
Rwork0.1563 56091 -
obs0.1571 58083 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129 Å2 / Biso mean: 35.1666 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.6→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 0 480 3277
Biso mean---43.59 -
Num. residues----354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.31841340.313764389895
1.64-1.680.30541400.263539554095100
1.68-1.730.24841420.227539884130100
1.73-1.790.26571410.210839774118100
1.79-1.850.20241420.186539904132100
1.85-1.930.20631420.17240144156100
1.93-2.020.21241410.171439694110100
2.02-2.120.2031420.161640134155100
2.12-2.260.16821430.154940144157100
2.26-2.430.17151430.151240224165100
2.43-2.670.18851430.14840324175100
2.67-3.060.16771430.150740444187100
3.06-3.860.14711460.136340854231100
3.86-44.120.1551500.141442244374100
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)
17.23494.85881.26886.36580.82932.1867-0.12280.08010.1604-0.0630.00240.0719-0.2285-0.02630.15450.19240.0229-0.04440.15580.02970.1067-0.3312.363915.6453
21.05140.0492-0.05291.3717-0.36181.9476-0.0923-0.04980.0267-0.0452-0.0409-0.0194-0.0679-0.04640.12320.13640.005-0.02770.14170.00490.1431-0.33264.223117.6689
33.31072.6726-4.25386.3285-3.68095.5239-0.4740.4843-0.3996-0.80880.0296-0.63730.97620.03860.45410.2482-0.00010.03090.37380.03230.261313.9922-2.245514.5226
48.2065.6808-4.48837.5682-5.11726.6537-0.253-0.0219-0.29740.0062-0.03340.09410.3259-0.16160.35320.1632-0.0159-0.03470.1517-0.01980.1310.2248-6.175723.3175
52.50840.2147-0.5911.1598-0.24182.456-0.03-0.11760.0491-0.0341-0.073-0.1589-0.08690.06820.09690.1809-0.0031-0.0290.1470.03760.18364.23674.455321.3986
62.2816-0.65120.28817.4416-2.14455.0508-0.0682-0.4263-0.1757-0.07990.02420.26810.1953-0.30880.06690.15410.01430.00630.27380.04860.147133.600916.685611.7438
74.5838-0.43170.10395.5202-2.38365.0239-0.0851-0.12920.0642-0.0827-0.2332-0.4359-0.0330.15010.2720.16190.0010.0110.14230.00540.163739.805122.28774.1224
82.5579-0.38270.05083.8655-2.24183.1666-0.0561-0.264-0.4908-0.6774-0.0869-0.44560.82640.08690.09670.36260.00830.05850.17260.04590.324937.476811.47073.7567
92.69870.3175-1.49143.6458-3.63986.6002-0.0269-0.2832-0.105-0.1287-0.2837-0.5280.1120.31840.32230.15890.01940.0010.19550.06750.281343.749118.03556.05
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 36 )A3 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 147 )A37 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 159 )A148 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 175 )A160 - 175
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 231 )A176 - 231
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 28 )B2 - 28
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 41 )B29 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 93 )B42 - 93
9X-RAY DIFFRACTION9chain 'B' and (resid 94 through 128 )B94 - 128

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