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- PDB-7e53: Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2... -

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Basic information

Entry
Database: PDB / ID: 7.0E+53
TitleCrystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution
Components
  • Green fluorescent protein
  • Green fluorescent protein's nanobody nb2
KeywordsFLUORESCENT PROTEIN / Aequorea victoria / Camelus bactrianus
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDing, Y. / Zhong, P.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070939 China
National Natural Science Foundation of China (NSFC)82030106 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural insights into two distinct nanobodies recognizing the same epitope of green fluorescent protein.
Authors: Zhong, P. / Wang, Z. / Cheng, S. / Zhang, Y. / Jiang, H. / Liu, R. / Ding, Y.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: Green fluorescent protein's nanobody nb2


Theoretical massNumber of molelcules
Total (without water)40,0832
Polymers40,0832
Non-polymers00
Water1,65792
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)64.207, 123.991, 108.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Green fluorescent protein


Mass: 26098.309 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 BL21(DE3) (bacteria) / References: UniProt: A0A059PIQ0
#2: Antibody Green fluorescent protein's nanobody nb2


Mass: 13984.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) Polyethylene glycol 400, 100mM CAPS/ Sodium hydroxide, pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 21347 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.086 / Rrim(I) all: 0.273 / Χ2: 0.958 / Net I/σ(I): 9.8 / Num. measured all: 133097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.10.46719430.340.2120.5171.38589.1
2.28-2.3730.40119570.2540.240.4710.73688.9
2.37-2.483.60.3820910.5270.2090.4380.78594.5
2.48-2.614.60.37220750.6850.1760.4140.86195.9
2.61-2.775.40.34721320.810.1470.3790.90596.8
2.77-2.996.10.3121840.9150.1210.3340.89298.6
2.99-3.296.80.27521860.9350.1020.2940.93798.7
3.29-3.768.50.27322040.9570.0890.2881.07898.7
3.76-4.7390.24722330.9540.080.260.98499
4.73-30100.24623420.9640.0770.2590.91399.4

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P, 6ITQ

2b3p

6itq


Resolution: 2.21→29.81 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 916 5 %
Rwork0.2037 17391 -
obs0.2065 18307 82.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.88 Å2 / Biso mean: 44.0677 Å2 / Biso min: 14.3 Å2
Refinement stepCycle: final / Resolution: 2.21→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 0 92 2875
Biso mean---36.55 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.320.378480.290680685427
2.32-2.470.3623940.28371953204766
2.47-2.660.28181540.27082695284990
2.66-2.930.33751440.25072935307998
2.93-3.350.27961480.21772960310898
3.35-4.220.24211580.18242975313398
4.22-29.810.2051700.1573067323797

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